Evolutionary law

@inproceedings{huxley1880on1,
    author = "Huxley, T. H",
    title = "On the application of the laws of evolution to the arrangement of the Vertebrata, and more particularly of the Mammalia",
    year = "1880",
    booktitle = "Proceedings of the Zoological Society of London, v. 43, p. 649-661",
    note = "talkorigins\_source = {true}; raw\_reference = {Huxley, T. H., 1880, On the application of the laws of evolution to the arrangement of the Vertebrata, and more particularly of the Mammalia: Proceedings of the Zoological Society of London, v. 43, p. 649-661.}"
}

@misc{kellogg1907darwinism2,
    author = "Kellogg, V. L",
    title = "Darwinism to-day",
    year = "1907",
    howpublished = "London, England, Bell \& Sons",
    note = "talkorigins\_source = {true}; raw\_reference = {Kellogg, V. L., 1907, Darwinism to-day: London, England, Bell \& Sons.}"
}

@article{crossref1923evolution,
    title = "Evolution and Darwinism",
    year = "1923",
    journal = "Science",
    url = "https://doi.org/10.1126/science.58.1499.xiv.s",
    doi = "10.1126/science.58.1499.xiv.s",
    number = "1499",
    openalex = "W4236935415",
    volume = "58"
}

@article{crossref1927evolution,
    title = "Evolution or Darwinism?",
    year = "1927",
    journal = "Blackfriars",
    url = "https://doi.org/10.1111/j.1741-2005.1927.tb04746.x",
    doi = "10.1111/j.1741-2005.1927.tb04746.x",
    number = "85",
    openalex = "W4233305340",
    pages = "241-246",
    volume = "8"
}

The Battle Lines in the evolution controversy had been clearly drawn by the year 1890. In scientific circles a few die-hards, like the German zoologist, Virchow, were making a last ditch fight against the increasingly popular Darwinian concept. American scientists, however, were virtually unanimous in their acceptance of evolution now that the restraining hand of Louis Aggassiz had been lifted. Among the theologians too might be found liberals who embraced the new theory; such influential Protestant preachers as Henry Ward Beecher and Lyman Abbott announced that they were “enthusiastic evolutionists.” Most Protestant leaders did not share this enthusiasm. They remained skeptical of evolution's scientific merits, suspicious of its philosophical implications, and fearful of its theological effects. Perhaps the most common Protestant technique was to denounce Darwinism as a threat to Christianity. Thus, as matters stood, America was in the midst of a struggle between a school of evolutionists, many of whom espoused unchristian or antichristian philosophies, and another group of anti-evolutionists who denied the scientific validity of evolution and objected to its theological implications. The evolutionists seemed to be gaining in strength and numbers.

@article{doi101017s0034670500003648,
    author = "Morrison, John L.",
    title = "William Seton — A Catholic Darwinist",
    year = "1959",
    journal = "The Review of Politics",
    abstract = "The Battle Lines in the evolution controversy had been clearly drawn by the year 1890. In scientific circles a few die-hards, like the German zoologist, Virchow, were making a last ditch fight against the increasingly popular Darwinian concept. American scientists, however, were virtually unanimous in their acceptance of evolution now that the restraining hand of Louis Aggassiz had been lifted. Among the theologians too might be found liberals who embraced the new theory; such influential Protestant preachers as Henry Ward Beecher and Lyman Abbott announced that they were “enthusiastic evolutionists.” Most Protestant leaders did not share this enthusiasm. They remained skeptical of evolution's scientific merits, suspicious of its philosophical implications, and fearful of its theological effects. Perhaps the most common Protestant technique was to denounce Darwinism as a threat to Christianity. Thus, as matters stood, America was in the midst of a struggle between a school of evolutionists, many of whom espoused unchristian or antichristian philosophies, and another group of anti-evolutionists who denied the scientific validity of evolution and objected to its theological implications. The evolutionists seemed to be gaining in strength and numbers.",
    url = "https://doi.org/10.1017/s0034670500003648",
    doi = "10.1017/s0034670500003648",
    openalex = "W2074060047",
    references = "crossref1923evolution"
}

@book{openalexw2556090403,
    author = "Moran, P. A. P.",
    title = "The statistical processes of evolutionary theory.",
    year = "1962",
    openalex = "W2556090403"
}

@article{openalexw2145250129,
    author = "Valen, Leigh Van",
    title = "A NEW EVOLUTIONARY LAW.",
    year = "1973",
    journal = "Medical Entomology and Zoology",
    openalex = "W2145250129"
}

@misc{vanvalen1973a3,
    author = "Van Valen, L",
    title = "A new evolutionary law",
    year = "1973",
    howpublished = "Evolutionary Theory, v. 1, p. 1-30",
    note = "talkorigins\_source = {true}; raw\_reference = {Van Valen, L., 1973, A new evolutionary law: Evolutionary Theory, v. 1, p. 1-30.}"
}

It is suggested that evolution in plants may be associated with the emergence of three primary strategies, each of which may be identified by reference to a number of characteristics including morphological features, resource allocation, phenology, and response to stress. The competitive strategy prevails in productive, relatively undisturbed vegetation, the stress-tolerant strategy is associated with continuously unproductive conditions, and the ruderal strategy is characteristic of severely disturbed but potentially productive habitats. A triangular model based upon the three strategies may be reconciled with the theory of r- and K-selection, provides an insight into the processes of vegetation succession and dominance, and appears to be capable of extension to fungi and to animals.

@article{doi101086283244,
    author = "Grime, J. P.",
    title = "Evidence for the Existence of Three Primary Strategies in Plants and Its Relevance to Ecological and Evolutionary Theory",
    year = "1977",
    journal = "The American Naturalist",
    abstract = "It is suggested that evolution in plants may be associated with the emergence of three primary strategies, each of which may be identified by reference to a number of characteristics including morphological features, resource allocation, phenology, and response to stress. The competitive strategy prevails in productive, relatively undisturbed vegetation, the stress-tolerant strategy is associated with continuously unproductive conditions, and the ruderal strategy is characteristic of severely disturbed but potentially productive habitats. A triangular model based upon the three strategies may be reconciled with the theory of r- and K-selection, provides an insight into the processes of vegetation succession and dominance, and appears to be capable of extension to fungi and to animals.",
    url = "https://doi.org/10.1086/283244",
    doi = "10.1086/283244",
    openalex = "W2055424972",
    references = "doi101038242344a0, doi101038250026a0, doi101086282454, doi101086282455, doi1015159781400881376, doi102307213332, doi1023072258728, doi10230725528056, doi1023073241344, doi105962bhltitle59991"
}

Abstract Contemporary mate preferences can provide important clues to human reproductive history. Little is known about which characteristics people value in potential mates. Five predictions were made about sex differences in human mate preferences based on evolutionary conceptions of parental investment, sexual selection, human reproductive capacity, and sexual asymmetries regarding certainty of paternity versus maternity. The predictions centered on how each sex valued earning capacity, ambition— industriousness, youth, physical attractiveness, and chastity. Predictions were tested in data from 37 samples drawn from 33 countries located on six continents and five islands (total N = 10,047). For 27 countries, demographic data on actual age at marriage provided a validity check on questionnaire data. Females were found to value cues to resource acquisition in potential mates more highly than males. Characteristics signaling reproductive capacity were valued more by males than by females. These sex differences may reflect different evolutionary selection pressures on human males and females; they provide powerful cross-cultural evidence of current sex differences in reproductive strategies. Discussion focuses on proximate mechanisms underlying mate preferences, consequences for human intrasexual competition, and the limitations of this study.

@article{doi101017s0140525x00023992,
    author = "Buss, David M.",
    title = "Sex differences in human mate preferences: Evolutionary hypotheses tested in 37 cultures",
    year = "1989",
    journal = "Behavioral and Brain Sciences",
    abstract = "Abstract Contemporary mate preferences can provide important clues to human reproductive history. Little is known about which characteristics people value in potential mates. Five predictions were made about sex differences in human mate preferences based on evolutionary conceptions of parental investment, sexual selection, human reproductive capacity, and sexual asymmetries regarding certainty of paternity versus maternity. The predictions centered on how each sex valued earning capacity, ambition— industriousness, youth, physical attractiveness, and chastity. Predictions were tested in data from 37 samples drawn from 33 countries located on six continents and five islands (total N = 10,047). For 27 countries, demographic data on actual age at marriage provided a validity check on questionnaire data. Females were found to value cues to resource acquisition in potential mates more highly than males. Characteristics signaling reproductive capacity were valued more by males than by females. These sex differences may reflect different evolutionary selection pressures on human males and females; they provide powerful cross-cultural evidence of current sex differences in reproductive strategies. Discussion focuses on proximate mechanisms underlying mate preferences, consequences for human intrasexual competition, and the limitations of this study.",
    url = "https://doi.org/10.1017/s0140525x00023992",
    doi = "10.1017/s0140525x00023992",
    openalex = "W2157338817",
    references = "doi101007978146847862422, doi1010160022519364900384, doi1010160022519366901846, doi1010160162309582900279, doi1010160162309583900274, doi101016s0065260122x00026, doi101017cbo9780511806292, doi101017s0140525x00010128, doi10103711774000, doi10103712293000, doi101038246015a0, doi101038369716c0, doi101086284064, doi101111j155856461957tb02911x, doi101126science327542, doi1011425786, doi1011770022022190211001, doi101537ase188722495, doi1023072393017, doi1023072412191, doi1023072485224, doi1023072576242, doi1023075530, doi102307582242, doi1043249781315129266, doi10432497813151292667, doi1043249781410606266, doi105962bhltitle27468, doi105962bhltitle59991, doi105962bhltitle82303, openalexw1649242647, openalexw2000871817"
}

@article{doi101038359826a0,
    author = "Nowak, Martin A. and May, Robert M.",
    title = "Evolutionary games and spatial chaos",
    year = "1992",
    journal = "Nature",
    url = "https://doi.org/10.1038/359826a0",
    doi = "10.1038/359826a0",
    openalex = "W2025490132",
    references = "doi101007978146847862422, doi101007bf00450633, doi101017cbo9780511806292, doi101038280445a0, doi102307257983"
}

This article proposes a contextual-evolutionary theory of human mating strategies. Both men and women are hypothesized to have evolved distinct psychological mechanisms that underlie short-term and long-term strategies. Men and women confront different adaptive problems in short-term as opposed to long-term mating contexts. Consequently, different mate preferences become activated from their strategic repertoires. Nine key hypotheses and 22 predictions from Sexual Strategies Theory are outlined and tested empirically. Adaptive problems sensitive to context include sexual accessibility, fertility assessment, commitment seeking and avoidance, immediate and enduring resource procurement, paternity certainty, assessment of mate value, and parental investment. Discussion summarizes 6 additional sources of behavioral data, outlines adaptive problems common to both sexes, and suggests additional contexts likely to cause shifts in mating strategy.

@article{doi1010370033295x1002204,
    author = "Buss, David M. and Schmitt, David P.",
    title = "Sexual Strategies Theory: An evolutionary perspective on human mating.",
    year = "1993",
    journal = "Psychological Review",
    abstract = "This article proposes a contextual-evolutionary theory of human mating strategies. Both men and women are hypothesized to have evolved distinct psychological mechanisms that underlie short-term and long-term strategies. Men and women confront different adaptive problems in short-term as opposed to long-term mating contexts. Consequently, different mate preferences become activated from their strategic repertoires. Nine key hypotheses and 22 predictions from Sexual Strategies Theory are outlined and tested empirically. Adaptive problems sensitive to context include sexual accessibility, fertility assessment, commitment seeking and avoidance, immediate and enduring resource procurement, paternity certainty, assessment of mate value, and parental investment. Discussion summarizes 6 additional sources of behavioral data, outlines adaptive problems common to both sexes, and suggests additional contexts likely to cause shifts in mating strategy.",
    url = "https://doi.org/10.1037/0033-295x.100.2.204",
    doi = "10.1037/0033-295x.100.2.204",
    openalex = "W1971871412",
    references = "doi1010160162309582900279, doi1010160162309583900274, doi101017s0140525x00023992, doi101126science7123238, doi101537ase188722495, doi1043249781315129266, openalexw1659631989, openalexw2000871817"
}

A phylogenetic framework inferred from comparisons of small subunit ribosomal RNA sequences describes the evolutionary origin and early branching patterns of the kingdom Animalia. Maximum likelihood analyses show the animal lineage is monophyletic and includes choanoflagellates. Within the metazoan assemblage, the divergence of sponges is followed by the Ctenophora, the Cnidaria plus the placozoan Trichoplax adhaerens, and finally by an unresolved polychotomy of bilateral animal phyla. From these data, it was inferred that animals and fungi share a unique evolutionary history and that their last common ancestor was a flagellated protist similar to extant choanoflagellates.

@article{doi101126science8469985,
    author = "Wainright, Patricia O. and Hinkle, Gregory and Sogin, Mitchell L. and Stickel, Shawn K.",
    title = "Monophyletic Origins of the Metazoa: an Evolutionary Link with Fungi",
    year = "1993",
    journal = "Science",
    abstract = "A phylogenetic framework inferred from comparisons of small subunit ribosomal RNA sequences describes the evolutionary origin and early branching patterns of the kingdom Animalia. Maximum likelihood analyses show the animal lineage is monophyletic and includes choanoflagellates. Within the metazoan assemblage, the divergence of sponges is followed by the Ctenophora, the Cnidaria plus the placozoan Trichoplax adhaerens, and finally by an unresolved polychotomy of bilateral animal phyla. From these data, it was inferred that animals and fungi share a unique evolutionary history and that their last common ancestor was a flagellated protist similar to extant choanoflagellates.",
    url = "https://doi.org/10.1126/science.8469985",
    doi = "10.1126/science.8469985",
    openalex = "W2034733986",
    references = "doi101126science3277277, openalexw2076004673"
}

Natural evolution is a population-based optimization process. Simulating this process on a computer results in stochastic optimization techniques that can often outperform classical methods of optimization when applied to difficult real-world problems. There are currently three main avenues of research in simulated evolution: genetic algorithms, evolution strategies, and evolutionary programming. Each method emphasizes a different facet of natural evolution. Genetic algorithms stress chromosomal operators. Evolution strategies emphasize behavioral changes at the level of the individual. Evolutionary programming stresses behavioral change at the level of the species. The development of each of these procedures over the past 35 years is described. Some recent efforts in these areas are reviewed.

@article{doi10110972265956,
    author = "Fogel, David B.",
    title = "An introduction to simulated evolutionary optimization",
    year = "1994",
    journal = "IEEE Transactions on Neural Networks",
    abstract = "Natural evolution is a population-based optimization process. Simulating this process on a computer results in stochastic optimization techniques that can often outperform classical methods of optimization when applied to difficult real-world problems. There are currently three main avenues of research in simulated evolution: genetic algorithms, evolution strategies, and evolutionary programming. Each method emphasizes a different facet of natural evolution. Genetic algorithms stress chromosomal operators. Evolution strategies emphasize behavioral changes at the level of the individual. Evolutionary programming stresses behavioral change at the level of the species. The development of each of these procedures over the past 35 years is described. Some recent efforts in these areas are reviewed.",
    url = "https://doi.org/10.1109/72.265956",
    doi = "10.1109/72.265956",
    openalex = "W2154808242",
    references = "doi1010079783662028308, doi101073pnas722646, doi101093auk1002507, doi101093genetics16297, doi104159harvard9780674865327, doi104324978100333479834, doi105860choice270936, doi107551mitpress10900010001, doi107551mitpress52360010001, openalexw1550375751, openalexw1965324089, openalexw2166843422"
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@article{doi101006dbio19960032,
    author = "Gilbert, Scott F. and Opitz, John M. and Raff, Rudolf A.",
    title = "Resynthesizing Evolutionary and Developmental Biology",
    year = "1996",
    journal = "Developmental Biology",
    url = "https://doi.org/10.1006/dbio.1996.0032",
    doi = "10.1006/dbio.1996.0032",
    openalex = "W2054702070",
    references = "doi105694j132653771943tb44800x, doi105962bhltitle21641"
}

TreeView is a simple, easy to use phylogenetic tree viewing utility that runs under both MacOS (on Apple Macintosh computers) and under Microsoft Windows on Intel based computers, the two most common personal computers used by biologists. Some phylogeny programs, such as PAUP (Swofford, 1993) and MacClade (Maddison and Maddison, 1992) already provide excellent tree drawing and printing facilities, however at present these programs are restricted to Apple Macintosh computers. Furthermore, they require the user to load a data set before any trees can be displayed which is inconvenient if the user simply wants to view the trees. More portable programs, such as DRAWGRAM and DRAWTREE in the PHYLIP package (Felsenstein, 1993) can run on both MacOS and Windows computers, but make little, if any use of the graphical interface features available under those operating systems. TreeView runs as a native application on either MacOS or Windows computers, enables the user to use the standard fonts installed on their machine, their printer, and supports the relevant native graphics format (PICT and Windows metafile) for either creating graphics files or pasting pictures to other applications via the clipboard. The program also supports standard file operations, such as 'drag and drop' whereby dragging a file's icon onto the program opens that file. TreeView can read a range of tree file formats (see below) and can display trees in a range of styles (Fig. 1). Additional information, such as edge lengths and internal node labels can also be displayed. The order of the terminal taxa in the tree can be altered, and the tree can be rerooted. If the tree file contains more than one tree the user can view each tree in turn. The program can also save trees in a variety of file formats, so that it can be used to move trees between programs that use different file formats.

@article{doi101093bioinformatics124357,
    author = "Page, Roderic",
    title = "Tree View: An application to display phylogenetic trees on personal computers",
    year = "1996",
    journal = "Computer applications in the biosciences",
    abstract = "TreeView is a simple, easy to use phylogenetic tree viewing utility that runs under both MacOS (on Apple Macintosh computers) and under Microsoft Windows on Intel based computers, the two most common personal computers used by biologists. Some phylogeny programs, such as PAUP (Swofford, 1993) and MacClade (Maddison and Maddison, 1992) already provide excellent tree drawing and printing facilities, however at present these programs are restricted to Apple Macintosh computers. Furthermore, they require the user to load a data set before any trees can be displayed which is inconvenient if the user simply wants to view the trees. More portable programs, such as DRAWGRAM and DRAWTREE in the PHYLIP package (Felsenstein, 1993) can run on both MacOS and Windows computers, but make little, if any use of the graphical interface features available under those operating systems. TreeView runs as a native application on either MacOS or Windows computers, enables the user to use the standard fonts installed on their machine, their printer, and supports the relevant native graphics format (PICT and Windows metafile) for either creating graphics files or pasting pictures to other applications via the clipboard. The program also supports standard file operations, such as 'drag and drop' whereby dragging a file's icon onto the program opens that file. TreeView can read a range of tree file formats (see below) and can display trees in a range of styles (Fig. 1). Additional information, such as edge lengths and internal node labels can also be displayed. The order of the terminal taxa in the tree can be altered, and the tree can be rerooted. If the tree file contains more than one tree the user can view each tree in turn. The program can also save trees in a variety of file formats, so that it can be used to move trees between programs that use different file formats.",
    url = "https://doi.org/10.1093/bioinformatics/12.4.357",
    doi = "10.1093/bioinformatics/12.4.357",
    openalex = "W2150297520",
    references = "doi101093bioinformatics10141, doi101093nar21133021, doi101093nar22224673, doi105860choice392183"
}

Every form of behaviour is shaped by trial and error. Such stepwise adaptation can occur through individual learning or through natural selection, the basis of evolution. Since the work of Maynard Smith and others, it has been realised how game theory can model this process. Evolutionary game theory replaces the static solutions of classical game theory by a dynamical approach centred not on the concept of rational players but on the population dynamics of behavioural programmes. In this book the authors investigate the nonlinear dynamics of the self-regulation of social and economic behaviour, and of the closely related interactions between species in ecological communities. Replicator equations describe how successful strategies spread and thereby create new conditions which can alter the basis of their success, i.e. to enable us to understand the strategic and genetic foundations of the endless chronicle of invasions and extinctions which punctuate evolution. In short, evolutionary game theory describes when to escalate a conflict, how to elicit cooperation, why to expect a balance of the sexes, and how to understand natural selection in mathematical terms.

@book{doi101017cbo9781139173179,
    author = "Hofbauer, Josef and Sigmund, Karl",
    title = "Evolutionary Games and Population Dynamics",
    year = "1998",
    booktitle = "Cambridge University Press eBooks",
    abstract = "Every form of behaviour is shaped by trial and error. Such stepwise adaptation can occur through individual learning or through natural selection, the basis of evolution. Since the work of Maynard Smith and others, it has been realised how game theory can model this process. Evolutionary game theory replaces the static solutions of classical game theory by a dynamical approach centred not on the concept of rational players but on the population dynamics of behavioural programmes. In this book the authors investigate the nonlinear dynamics of the self-regulation of social and economic behaviour, and of the closely related interactions between species in ecological communities. Replicator equations describe how successful strategies spread and thereby create new conditions which can alter the basis of their success, i.e. to enable us to understand the strategic and genetic foundations of the endless chronicle of invasions and extinctions which punctuate evolution. In short, evolutionary game theory describes when to escalate a conflict, how to elicit cooperation, why to expect a balance of the sexes, and how to understand natural selection in mathematical terms.",
    url = "https://doi.org/10.1017/cbo9781139173179",
    doi = "10.1017/cbo9781139173179",
    openalex = "W2085728653",
    references = "doi101007978146847862422, doi1010160040580977900429, doi101038119012b0, doi101086282272, doi1023071578, doi1023072965538, doi1023074549, doi1023075530, doi105962bhltitle4489"
}

Economists long have employed evolutionary language and metaphors to characterize economic change, but until recently have largely eschewed the expression of explicit evolutionary theories. Over the last decade, however, a number of explicit evolutionary theories have been developed by economists, and other social scientists. This essay discusses the general analytic art form, and summarizes and discusses a number of the particular models. In the light of those examples, it evaluates the strengths and weaknesses of explicit evolutionary theorizing as an approach to understanding economic change.

@incollection{doi10100797833228084005,
    author = "Nelson, Richard Alan",
    title = "Recent Evolutionary Theorizing About Economic Change",
    year = "2000",
    booktitle = "VS Verlag für Sozialwissenschaften eBooks",
    abstract = "Economists long have employed evolutionary language and metaphors to characterize economic change, but until recently have largely eschewed the expression of explicit evolutionary theories. Over the last decade, however, a number of explicit evolutionary theories have been developed by economists, and other social scientists. This essay discusses the general analytic art form, and summarizes and discusses a number of the particular models. In the light of those examples, it evaluates the strengths and weaknesses of explicit evolutionary theorizing as an approach to understanding economic change.",
    url = "https://doi.org/10.1007/978-3-322-80840-0\_5",
    doi = "10.1007/978-3-322-80840-0\_5",
    openalex = "W1521985566",
    references = "doi101007978146847862422, doi10106313050879, doi10108000213624198711504638, doi101093oxfordjournalscjea013725, doi1011425786, doi1023071058511, doi1023071060065, doi1023071884513, doi1023072218271, doi1023072232409, doi1023072233763, doi1023072234208, doi1023072393344, doi1023072393549, doi1023072551371, doi1023072938222, doi107208chicago97802263604920010001"
}

Phylogenies reconstructed from gene sequences can be used to investigate the tempo and mode of species diversification. Here we develop and use new statistical methods to infer past patterns of speciation and extinction from molecular phylogenies. Specifically, we test the null hypothesis that per-lineage speciation and extinction rates have remained constant through time. Rejection of this hypothesis may provide evidence for evolutionary events such as adaptive radiations or key adaptations. In contrast to previous approaches, our methods are robust to incomplete taxon sampling and are conservative with respect to extinction. Using simulation we investigate, first, the adverse effects of failing to take incomplete sampling into account and, second, the power and reliability of our tests. When applied to published phylogenies our tests suggest that, in some cases, speciation rates have decreased through time.

@article{doi101098rspb20001278,
    author = "Pybus, Oliver G. and Harvey, Paul",
    title = "Testing macro–evolutionary models using incomplete molecular phylogenies",
    year = "2000",
    journal = "Proceedings of the Royal Society B Biological Sciences",
    abstract = "Phylogenies reconstructed from gene sequences can be used to investigate the tempo and mode of species diversification. Here we develop and use new statistical methods to infer past patterns of speciation and extinction from molecular phylogenies. Specifically, we test the null hypothesis that per-lineage speciation and extinction rates have remained constant through time. Rejection of this hypothesis may provide evidence for evolutionary events such as adaptive radiations or key adaptations. In contrast to previous approaches, our methods are robust to incomplete taxon sampling and are conservative with respect to extinction. Using simulation we investigate, first, the adverse effects of failing to take incomplete sampling into account and, second, the power and reliability of our tests. When applied to published phylogenies our tests suggest that, in some cases, speciation rates have decreased through time.",
    url = "https://doi.org/10.1098/rspb.2000.1278",
    doi = "10.1098/rspb.2000.1278",
    openalex = "W2118610143",
    references = "doi101086627905"
}

@misc{crossref2001darwinism,
    title = "Darwinism and Evolutionary Economics",
    year = "2001",
    url = "https://doi.org/10.4337/9781843762942",
    doi = "10.4337/9781843762942"
}

s.kumar@asu.edu

@article{doi101093bioinformatics17121244,
    author = "Kumar, Sudhir and Tamura, Koichiro and Jakobsen, Ingrid B. and Nei, Masatoshi",
    title = "MEGA2: molecular evolutionary genetics analysis software",
    year = "2001",
    journal = "Bioinformatics",
    abstract = "s.kumar@asu.edu",
    url = "https://doi.org/10.1093/bioinformatics/17.12.1244",
    doi = "10.1093/bioinformatics/17.12.1244",
    openalex = "W2156434383",
    references = "doi101007bf00173196, doi101093bioinformatics102189, doi101093oso97801951358480010001, doi101093oxfordjournalsmolbeva040259, doi102307jctvcm4gbm10, openalexw2002446259"
}

@article{doi101016s0045782501003231,
    author = "Coello, Carlos A. Coello",
    title = "Theoretical and numerical constraint-handling techniques used with evolutionary algorithms: a survey of the state of the art",
    year = "2002",
    journal = "Computer Methods in Applied Mechanics and Engineering",
    url = "https://doi.org/10.1016/s0045-7825(01)00323-1",
    doi = "10.1016/s0045-7825(01)00323-1",
    openalex = "W2167580870",
    references = "doi1010079783662028308, doi1010160378475482901173, doi105962bhltitle59991, doi107551mitpress39270010001, openalexw1511493290"
}

@book{doi102307jctvjsf433,
    author = "Gould, Stephen Jay",
    title = "The Structure of Evolutionary Theory",
    year = "2002",
    booktitle = "Harvard University Press eBooks",
    url = "https://doi.org/10.2307/j.ctvjsf433",
    doi = "10.2307/j.ctvjsf433",
    openalex = "W4300925890"
}

* *1. Defining and Revising the Structure of Evolutionary Theory * Part I: The History of Darwinian Logic and Debate *2. The Essence of Darwinism and the Basis of Modern Orthodoxy: An Exegesis of the Origin of Species *3. Seeds of Hierarchy *4. Internalism and Laws of Form: Pre-Darwinian Alternatives to Functionalism *5. The Fruitful Facets of Galton's Polyhedron: Channels and Saltations in Post-Darwinian Formalism *6. Pattern and Progress on the Geological Stage *7. The Modern Synthesis as a Limited Consensus * Part II: Towards a Revised and Expanded Evolutionary Theory *8. Species as Individuals in the Hierarchical Theory of Selection *9. Punctuated Equilibrium and the Validation of Macroevolutionary Theory *10. The Integration of Constraint and Adaptation (Structure and Function) in Ontogeny and Phylogeny: Historical Constraints and the Evolution of Development *11. The Integration of Constraint and Adaptation (Structure and Function) in Ontogeny and Phylogeny: Structural Constraints, Spandrels, and the Centrality of Exaptation in Macroevolution *12. Tiers of Time and Trials of Extrapolationism, With an Epilog on the Interaction of General Theory and Contingent History * Bibliography * Index

@article{doi105860choice396411,
    author = "Gould, Stephen Jay",
    title = "The structure of evolutionary theory",
    year = "2002",
    journal = "Choice Reviews Online",
    abstract = "* *1. Defining and Revising the Structure of Evolutionary Theory * Part I: The History of Darwinian Logic and Debate *2. The Essence of Darwinism and the Basis of Modern Orthodoxy: An Exegesis of the Origin of Species *3. Seeds of Hierarchy *4. Internalism and Laws of Form: Pre-Darwinian Alternatives to Functionalism *5. The Fruitful Facets of Galton's Polyhedron: Channels and Saltations in Post-Darwinian Formalism *6. Pattern and Progress on the Geological Stage *7. The Modern Synthesis as a Limited Consensus * Part II: Towards a Revised and Expanded Evolutionary Theory *8. Species as Individuals in the Hierarchical Theory of Selection *9. Punctuated Equilibrium and the Validation of Macroevolutionary Theory *10. The Integration of Constraint and Adaptation (Structure and Function) in Ontogeny and Phylogeny: Historical Constraints and the Evolution of Development *11. The Integration of Constraint and Adaptation (Structure and Function) in Ontogeny and Phylogeny: Structural Constraints, Spandrels, and the Centrality of Exaptation in Macroevolution *12. Tiers of Time and Trials of Extrapolationism, With an Epilog on the Interaction of General Theory and Contingent History * Bibliography * Index",
    url = "https://doi.org/10.5860/choice.39-6411",
    doi = "10.5860/choice.39-6411",
    openalex = "W1539968307"
}

@article{doi101016jtree200404009,
    author = "Sih, Andrew and Bell, Alison M. and Johnson, J. Chadwick",
    title = "Behavioral syndromes: an ecological and evolutionary overview",
    year = "2004",
    journal = "Trends in Ecology \& Evolution",
    url = "https://doi.org/10.1016/j.tree.2004.04.009",
    doi = "10.1016/j.tree.2004.04.009",
    openalex = "W2109104251",
    references = "doi101007978146847862422, doi101017cbo9780511806292, doi101073pnas931910262"
}

With its theoretical basis firmly established in molecular evolutionary and population genetics, the comparative DNA and protein sequence analysis plays a central role in reconstructing the evolutionary histories of species and multigene families, estimating rates of molecular evolution, and inferring the nature and extent of selective forces shaping the evolution of genes and genomes. The scope of these investigations has now expanded greatly owing to the development of high-throughput sequencing techniques and novel statistical and computational methods. These methods require easy-to-use computer programs. One such effort has been to produce Molecular Evolutionary Genetics Analysis (MEGA) software, with its focus on facilitating the exploration and analysis of the DNA and protein sequence variation from an evolutionary perspective. Currently in its third major release, MEGA3 contains facilities for automatic and manual sequence alignment, web-based mining of databases, inference of the phylogenetic trees, estimation of evolutionary distances and testing evolutionary hypotheses. This paper provides an overview of the statistical methods, computational tools, and visual exploration modules for data input and the results obtainable in MEGA.

@article{doi101093bib52150,
    author = "Kumar, Sudhir",
    title = "MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment",
    year = "2004",
    journal = "Briefings in Bioinformatics",
    abstract = "With its theoretical basis firmly established in molecular evolutionary and population genetics, the comparative DNA and protein sequence analysis plays a central role in reconstructing the evolutionary histories of species and multigene families, estimating rates of molecular evolution, and inferring the nature and extent of selective forces shaping the evolution of genes and genomes. The scope of these investigations has now expanded greatly owing to the development of high-throughput sequencing techniques and novel statistical and computational methods. These methods require easy-to-use computer programs. One such effort has been to produce Molecular Evolutionary Genetics Analysis (MEGA) software, with its focus on facilitating the exploration and analysis of the DNA and protein sequence variation from an evolutionary perspective. Currently in its third major release, MEGA3 contains facilities for automatic and manual sequence alignment, web-based mining of databases, inference of the phylogenetic trees, estimation of evolutionary distances and testing evolutionary hypotheses. This paper provides an overview of the statistical methods, computational tools, and visual exploration modules for data input and the results obtainable in MEGA.",
    url = "https://doi.org/10.1093/bib/5.2.150",
    doi = "10.1093/bib/5.2.150",
    openalex = "W2146396346",
    references = "doi101007bf01731581, doi101007bf02407308, doi101016b9781483232119500097, doi101093bioinformatics17121244, doi101093genetics1233585, doi101093nar22224673, doi101093nar25173389, doi101093oso97801951358480010001, doi101093oxfordjournalsmolbeva040023, doi101093oxfordjournalsmolbeva040259, doi101093oxfordjournalsmolbeva040343, doi101093oxfordjournalsmolbeva040410, doi101093oxfordjournalsmolbeva040454, doi101093oxfordjournalsmolbeva040771, doi101111j155856461985tb00420x, doi1023072408678, doi1023072412074, doi105860choice392183, openalexw2032279931, openalexw3217097258"
}

Evolutionary theory is enjoying a renaissance; in many disciplines, including economics, there has been a substantial flourishing of ideas that does much more than pay scholarly homage to one of the principal scientific developments of all time. For economists interested in innovation, competition, growth and development, an interest in the evolutionary idea is not difficult to establish; for the central empirical fact of the past two centuries, if not longer, has been sustained change and transformation in the patterns of activities that define modern economies. The evidence is pervasive and compelling. The creation of new activities, the demise of established ones and the constant shifts in the economic importance of surviving activities are ever-present symbols of the changes taking place in many different locations at different rates. The structural and qualitative transformations they produce in our economic world in comparatively short spaces of time are remarkable indeed – nothing less than a continuous remodelling and shifting around of the economic furniture.

@incollection{doi101017cbo9780511492297012,
    author = "Metcalfe, J. Stanley",
    title = "Evolutionary concepts in relation to evolutionary economics",
    year = "2005",
    booktitle = "Cambridge University Press eBooks",
    abstract = "Evolutionary theory is enjoying a renaissance; in many disciplines, including economics, there has been a substantial flourishing of ideas that does much more than pay scholarly homage to one of the principal scientific developments of all time. For economists interested in innovation, competition, growth and development, an interest in the evolutionary idea is not difficult to establish; for the central empirical fact of the past two centuries, if not longer, has been sustained change and transformation in the patterns of activities that define modern economies. The evidence is pervasive and compelling. The creation of new activities, the demise of established ones and the constant shifts in the economic importance of surviving activities are ever-present symbols of the changes taking place in many different locations at different rates. The structural and qualitative transformations they produce in our economic world in comparatively short spaces of time are remarkable indeed – nothing less than a continuous remodelling and shifting around of the economic furniture.",
    url = "https://doi.org/10.1017/cbo9780511492297.012",
    doi = "10.1017/cbo9780511492297.012",
    openalex = "W2491636393",
    references = "crossref2001darwinism"
}

Trees do not form a natural group but share attributes such as great size, longevity, and high reproductive output that affect their mode and tempo of evolution. In particular, trees are unique in that they maintain high levels of diversity while accumulating new mutations only slowly. They are also capable of rapid local adaptation and can evolve quickly from nontree ancestors, but most existing tree lineages typically experience low speciation and extinction rates. We discuss why the tree growth habit should lead to these seemingly paradoxical features.

@article{doi101146annurevecolsys37091305110215,
    author = "Petit, Rémy J. and Hampe, Arndt",
    title = "Some Evolutionary Consequences of Being a Tree",
    year = "2006",
    journal = "Annual Review of Ecology Evolution and Systematics",
    abstract = "Trees do not form a natural group but share attributes such as great size, longevity, and high reproductive output that affect their mode and tempo of evolution. In particular, trees are unique in that they maintain high levels of diversity while accumulating new mutations only slowly. They are also capable of rapid local adaptation and can evolve quickly from nontree ancestors, but most existing tree lineages typically experience low speciation and extinction rates. We discuss why the tree growth habit should lead to these seemingly paradoxical features.",
    url = "https://doi.org/10.1146/annurev.ecolsys.37.091305.110215",
    doi = "10.1146/annurev.ecolsys.37.091305.110215",
    openalex = "W2102352162",
    references = "doi101111j001438202001tb00826x, doi101111j14610248200500739x, doi101126science1061967, doi101146annurevecolsys271237, doi101146annureves10110179001133, doi101146annureves15110184000433, doi107208chicago97802261186970010001, openalexw2065039187, openalexw2145250129, openalexw2146778590"
}

Traditional problems solving methodologies like brainstorming, synectics, trial and error, etc. find their limits when they are facing inventive problems or problems that could be described like contradictions. A contradiction exists when two different and mutually exclusive requirements, states or conditions in a system, have to be present and act together, with the aim to accomplish same objectives. Trade off is usually the most used way to solve this kind of problem, also characterized by a random search of solutions. These situations have a negative impact over performance, which could be improved by applying other methodologies and tools. The theory of inventive problem solving or TRIZ theory has the capacity to eliminate these negative aspects described above and to produce innovative solutions to contradictions. This approach, which is different from the traditional psychology based approaches, is knowledge based. The particular vision of TRIZ is based on the history of technological evolution. TRIZ considers innovation like a process which can be controlled and deployed systematically. Paradoxically, this knowledge based approach with transversal domain application, does not have the capacity to memorise, which is fundamental for learning. Consequently, knowledge that has been employed and created while solving inventive problems can not be reused. This drawback has a negative effect on problem solving performance while deploying TRIZ. Knowledge management has developed the capacity to identify, store and reuse knowledge. This is the core capacity of several knowledge management methodologies, among them is, the Case-Based Reasoning (CBR). The performance of this problem solving tool, lies essentially in its capacity to offer a pragmatic answer for specific domain problems. CBR systems solve a new problem by identifying its similarity to one or several previously solved problems stored in a memory and by adapting their known solutions. Since CBR application is domain specific, CBR cannot consider the solutions that have already been identified in others domains while solving new problems. This characteristic limits the CBR’s capacity to propose innovative solutions to a problem. Besides, a shortcoming is revealed when a CBR system faces a problem that had not been solved in the past. If this situation occurs, the memory cannot find a similar problem and consequently, no solution is proposed. The limits and the complementarity observed between TRIZ and CBR are employed to propose a new model. This model presents an approach that combines the technological vision of TRIZ and the ability developed by CBR to memorize and to reuse knowledge. This synergy allows in the fist place, to steer the creative effort when facing inventive problems and in the second, to reuse knowledge that had been acquired in past problems. The capability of this new approach is illustrated by its application in process engineering and industrial engineering.

@phdthesis{openalexw134840284,
    author = "Cortés-Robles, Guillermo",
    title = "Management de l'innovation technologique et des connaissances: synergie entre la théorie TRIZ et le raisonnement à partir de cas: application en génie des procédés et systèmes industriels",
    year = "2006",
    booktitle = "SPIRE - Sciences Po Institutional REpository",
    abstract = "Traditional problems solving methodologies like brainstorming, synectics, trial and error, etc. find their limits when they are facing inventive problems or problems that could be described like contradictions. A contradiction exists when two different and mutually exclusive requirements, states or conditions in a system, have to be present and act together, with the aim to accomplish same objectives. Trade off is usually the most used way to solve this kind of problem, also characterized by a random search of solutions. These situations have a negative impact over performance, which could be improved by applying other methodologies and tools. The theory of inventive problem solving or TRIZ theory has the capacity to eliminate these negative aspects described above and to produce innovative solutions to contradictions. This approach, which is different from the traditional psychology based approaches, is knowledge based. The particular vision of TRIZ is based on the history of technological evolution. TRIZ considers innovation like a process which can be controlled and deployed systematically. Paradoxically, this knowledge based approach with transversal domain application, does not have the capacity to memorise, which is fundamental for learning. Consequently, knowledge that has been employed and created while solving inventive problems can not be reused. This drawback has a negative effect on problem solving performance while deploying TRIZ. Knowledge management has developed the capacity to identify, store and reuse knowledge. This is the core capacity of several knowledge management methodologies, among them is, the Case-Based Reasoning (CBR). The performance of this problem solving tool, lies essentially in its capacity to offer a pragmatic answer for specific domain problems. CBR systems solve a new problem by identifying its similarity to one or several previously solved problems stored in a memory and by adapting their known solutions. Since CBR application is domain specific, CBR cannot consider the solutions that have already been identified in others domains while solving new problems. This characteristic limits the CBR’s capacity to propose innovative solutions to a problem. Besides, a shortcoming is revealed when a CBR system faces a problem that had not been solved in the past. If this situation occurs, the memory cannot find a similar problem and consequently, no solution is proposed. The limits and the complementarity observed between TRIZ and CBR are employed to propose a new model. This model presents an approach that combines the technological vision of TRIZ and the ability developed by CBR to memorize and to reuse knowledge. This synergy allows in the fist place, to steer the creative effort when facing inventive problems and in the second, to reuse knowledge that had been acquired in past problems. The capability of this new approach is illustrated by its application in process engineering and industrial engineering.",
    openalex = "W134840284"
}

@article{ryan2006the,
    author = "Ryan, Frank X.",
    title = "The evolution of Darwinism: Selection, adaptation, and progress in evolutionary biology",
    year = "2006",
    journal = "Journal of the History of the Behavioral Sciences",
    url = "https://doi.org/10.1002/jhbs.20149",
    doi = "10.1002/jhbs.20149",
    number = "2",
    openalex = "W1991686317",
    pages = "193-194",
    volume = "42"
}

In this article, the use of the niche concept for explaining radical technical change is explored. Contributions of various strands of literatures are elaborated and systematized in a taxonomy. Radical change or technological discontinuity is defined as the establishment of a new sociotechnical regime. Sociotechnical regimes carry and store rules for how to produce, use and regulate specific technologies. They perform the task of genes and define the boundary between technological species. It is proposed that radical change is generated by four different evolutionary mechanisms and patterns: natural selection, punctuated equilibrium, market niche selection, and technological niche selection. In each pattern, a different type of niche is implicated in the change process. The difference between niches results from differentiating between two dimensions: (1) whether niches are internal or external to the prevailing sociotechnical regime; (2) whether rules for design and use of a specific technology are stable or unstable within the niche.

@article{doi101007s0019100700575,
    author = "Schot, Johan and Geels, Frank W.",
    title = "Niches in evolutionary theories of technical change",
    year = "2007",
    journal = "Journal of Evolutionary Economics",
    abstract = "In this article, the use of the niche concept for explaining radical technical change is explored. Contributions of various strands of literatures are elaborated and systematized in a taxonomy. Radical change or technological discontinuity is defined as the establishment of a new sociotechnical regime. Sociotechnical regimes carry and store rules for how to produce, use and regulate specific technologies. They perform the task of genes and define the boundary between technological species. It is proposed that radical change is generated by four different evolutionary mechanisms and patterns: natural selection, punctuated equilibrium, market niche selection, and technological niche selection. In each pattern, a different type of niche is implicated in the change process. The difference between niches results from differentiating between two dimensions: (1) whether niches are internal or external to the prevailing sociotechnical regime; (2) whether rules for design and use of a specific technology are stable or unstable within the niche.",
    url = "https://doi.org/10.1007/s00191-007-0057-5",
    doi = "10.1007/s00191-007-0057-5",
    openalex = "W1569479704",
    references = "crossref2001darwinism"
}

@article{doi101016jphysrep200704004,
    author = "Szabó, György and Fáth, Gábor",
    title = "Evolutionary games on graphs",
    year = "2007",
    journal = "Physics Reports",
    url = "https://doi.org/10.1016/j.physrep.2007.04.004",
    doi = "10.1016/j.physrep.2007.04.004",
    openalex = "W1992195122",
    references = "doi1010160022519364900384, doi1010160022519364900396, doi101017cbo9780511806292, doi101038246015a0, doi10103830918, doi101038366223a0, doi101038nature00823, doi101038nature03607, doi101090mbk12132, doi101098rspa19270118, doi101103revmodphys65851, doi101103revmodphys7447, doi10111911934457, doi10111911986710, doi101126science16238591243, doi101126science2865439509, doi101126science7466396, doi1011370129022, doi101137s003614450342480, doi1015159780691213255, doi1015159780691213255004, doi1023072256497, doi1023072341823, doi102307257983, doi102307jctvjghw98, doi105962bhltitle27468, openalexw2040525210, openalexw2624262714"
}

@article{doi101038nature05587,
    author = "Forest, Félix and Grenyer, Richard and Rouget, Mathieu and Davies, T. Jonathan and Cowling, Richard M. and Faith, Daniel P. and Balmford, Andrew and Manning, John C. and Procheş, Şerban and van der Bank, Michelle and Reeves, Gail and Hedderson, Terry A. and Savolainen, Vincent",
    title = "Preserving the evolutionary potential of floras in biodiversity hotspots",
    year = "2007",
    journal = "Nature",
    url = "https://doi.org/10.1038/nature05587",
    doi = "10.1038/nature05587",
    openalex = "W2140483939",
    references = "doi101017s1464793103006171, doi101111j109600311999tb00277x"
}

Ever since an “evolutionary” perspective on the economy has been suggested, there have been differing, and partly incommensurable, views on what specifically this means. By working out where the differences lie and what motivates them, this paper identifies four major approaches to evolutionary economics. The differences between them can be traced back to opposite positions regarding the basic assumptions about reality and the proper conceptualization of evolution. The same differences can also be found in evolutionary game theory. Achievements of the major approaches to evolutionary economics and their prospects for future research are assessed by means of a peer survey.

@article{doi101007s0019100801077,
    author = "Witt, Ulrich",
    title = "What is specific about evolutionary economics?",
    year = "2008",
    journal = "Journal of Evolutionary Economics",
    abstract = "Ever since an “evolutionary” perspective on the economy has been suggested, there have been differing, and partly incommensurable, views on what specifically this means. By working out where the differences lie and what motivates them, this paper identifies four major approaches to evolutionary economics. The differences between them can be traced back to opposite positions regarding the basic assumptions about reality and the proper conceptualization of evolution. The same differences can also be found in evolutionary game theory. Achievements of the major approaches to evolutionary economics and their prospects for future research are assessed by means of a peer survey.",
    url = "https://doi.org/10.1007/s00191-008-0107-7",
    doi = "10.1007/s00191-008-0107-7",
    openalex = "W2063903232",
    references = "crossref2001darwinism, doi101007s001910050058, doi104337978184542350600007"
}

Charles Darwin sketched his first evolutionary tree in 1837, and trees have remained a central metaphor in evolutionary biology up to the present. Today, phylogenetics—the science of constructing and evaluating hypotheses about historical patterns of descent in the form of evolutionary trees—has become pervasive within and increasingly outside evolutionary biology. Fostering skills in “tree thinking” is therefore a critical component of biological education. Conversely, misconceptions about evolutionary trees can be very detrimental to one’s understanding of the patterns and processes that have occurred in the history of life. This paper provides a basic introduction to evolutionary trees, including some guidelines for how and how not to read them. Ten of the most common misconceptions about evolutionary trees and their implications for understanding evolution are addressed.

@article{doi101007s120520080035x,
    author = "Gregory, T. Ryan",
    title = "Understanding Evolutionary Trees",
    year = "2008",
    journal = "Evolution Education and Outreach",
    abstract = "Charles Darwin sketched his first evolutionary tree in 1837, and trees have remained a central metaphor in evolutionary biology up to the present. Today, phylogenetics—the science of constructing and evaluating hypotheses about historical patterns of descent in the form of evolutionary trees—has become pervasive within and increasingly outside evolutionary biology. Fostering skills in “tree thinking” is therefore a critical component of biological education. Conversely, misconceptions about evolutionary trees can be very detrimental to one’s understanding of the patterns and processes that have occurred in the history of life. This paper provides a basic introduction to evolutionary trees, including some guidelines for how and how not to read them. Ten of the most common misconceptions about evolutionary trees and their implications for understanding evolution are addressed.",
    url = "https://doi.org/10.1007/s12052-008-0035-x",
    doi = "10.1007/s12052-008-0035-x",
    openalex = "W2158798844",
    references = "doi101038nature05634, doi101086383584, doi101093oso97801951358480010001, doi101126science1126746, doi1023073037993, doi102307jctvjsf433, doi105860choice396411, doi105962bhltitle59991, openalexw2002446259, openalexw3135630760"
}

@article{doi101016jcell200806030,
    author = "Carroll, Sean B.",
    title = "Evo-Devo and an Expanding Evolutionary Synthesis: A Genetic Theory of Morphological Evolution",
    year = "2008",
    journal = "Cell",
    url = "https://doi.org/10.1016/j.cell.2008.06.030",
    doi = "10.1016/j.cell.2008.06.030",
    openalex = "W2171193618",
    references = "doi1010079783642866593, doi101016b9781483227344500176, doi101038276565a0, doi101038376479a0, doi10103841710, doi101038nature02415, doi101038nature03158, doi101038nrg2063, doi101086406830, doi101111j001438202000tb00544x, doi101111j15585646200700105x, doi101126science1090005, doi101126science1107239, doi101126science147365368, doi101126science7892602, doi101242dev1212333, doi101371journalpbio0030245, doi105860choice395182, openalexw591049712, openalexw614012683"
}

A recent advance in the phylogenetic comparative analysis of continuous traits has been explicit, model-based measurement of "phylogenetic signal" in data sets composed of observations collected from species related by a phylogenetic tree. Phylogenetic signal is a measure of the statistical dependence among species' trait values due to their phylogenetic relationships. Although phylogenetic signal is a measure of pattern (statistical dependence), there has nonetheless been a widespread propensity in the literature to attribute this pattern to aspects of the evolutionary process or rate. This may be due, in part, to the perception that high evolutionary rate necessarily results in low phylogenetic signal; and, conversely, that low evolutionary rate or stabilizing selection results in high phylogenetic signal (due to the resulting high resemblance between related species). In this study, we use individual-based numerical simulations on stochastic phylogenetic trees to clarify the relationship between phylogenetic signal, rate, and evolutionary process. Under the simplest model for quantitative trait evolution, homogeneous rate genetic drift, there is no relation between evolutionary rate and phylogenetic signal. For other circumstances, such as functional constraint, fluctuating selection, niche conservatism, and evolutionary heterogeneity, the relationship between process, rate, and phylogenetic signal is complex. For these reasons, we recommend against interpretations of evolutionary process or rate based on estimates of phylogenetic signal.

@article{doi10108010635150802302427,
    author = "Revell, Liam J. and Harmon, Luke J. and Collar, David C.",
    title = "Phylogenetic Signal, Evolutionary Process, and Rate",
    year = "2008",
    journal = "Systematic Biology",
    abstract = {A recent advance in the phylogenetic comparative analysis of continuous traits has been explicit, model-based measurement of "phylogenetic signal" in data sets composed of observations collected from species related by a phylogenetic tree. Phylogenetic signal is a measure of the statistical dependence among species' trait values due to their phylogenetic relationships. Although phylogenetic signal is a measure of pattern (statistical dependence), there has nonetheless been a widespread propensity in the literature to attribute this pattern to aspects of the evolutionary process or rate. This may be due, in part, to the perception that high evolutionary rate necessarily results in low phylogenetic signal; and, conversely, that low evolutionary rate or stabilizing selection results in high phylogenetic signal (due to the resulting high resemblance between related species). In this study, we use individual-based numerical simulations on stochastic phylogenetic trees to clarify the relationship between phylogenetic signal, rate, and evolutionary process. Under the simplest model for quantitative trait evolution, homogeneous rate genetic drift, there is no relation between evolutionary rate and phylogenetic signal. For other circumstances, such as functional constraint, fluctuating selection, niche conservatism, and evolutionary heterogeneity, the relationship between process, rate, and phylogenetic signal is complex. For these reasons, we recommend against interpretations of evolutionary process or rate based on estimates of phylogenetic signal.},
    url = "https://doi.org/10.1080/10635150802302427",
    doi = "10.1080/10635150802302427",
    openalex = "W2162399971",
    references = "doi101038217624a0, doi10103844766, doi101073pnas0507648103, doi101086284325, doi101086383584, doi101086510633, doi101093oso97801985052350010001, doi101093oso97801985464120010001, doi101111j001438202001tb00731x, doi101111j001438202003tb00285x, doi1023072529912, doi102307jctvjsf433, doi105860choice295104, doi105860choice396411"
}

The Molecular Evolutionary Genetics Analysis (MEGA) software is a desktop application designed for comparative analysis of homologous gene sequences either from multigene families or from different species with a special emphasis on inferring evolutionary relationships and patterns of DNA and protein evolution. In addition to the tools for statistical analysis of data, MEGA provides many convenient facilities for the assembly of sequence data sets from files or web-based repositories, and it includes tools for visual presentation of the results obtained in the form of interactive phylogenetic trees and evolutionary distance matrices. Here we discuss the motivation, design principles and priorities that have shaped the development of MEGA. We also discuss how MEGA might evolve in the future to assist researchers in their growing need to analyze large data set using new computational methods.

@article{doi101093bibbbn017,
    author = "Kumar, Sudhir and Nei, M and Dudley, Joel T. and Tamura, Koichiro",
    title = "MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences",
    year = "2008",
    journal = "Briefings in Bioinformatics",
    abstract = "The Molecular Evolutionary Genetics Analysis (MEGA) software is a desktop application designed for comparative analysis of homologous gene sequences either from multigene families or from different species with a special emphasis on inferring evolutionary relationships and patterns of DNA and protein evolution. In addition to the tools for statistical analysis of data, MEGA provides many convenient facilities for the assembly of sequence data sets from files or web-based repositories, and it includes tools for visual presentation of the results obtained in the form of interactive phylogenetic trees and evolutionary distance matrices. Here we discuss the motivation, design principles and priorities that have shaped the development of MEGA. We also discuss how MEGA might evolve in the future to assist researchers in their growing need to analyze large data set using new computational methods.",
    url = "https://doi.org/10.1093/bib/bbn017",
    doi = "10.1093/bib/bbn017",
    openalex = "W2110899053",
    references = "doi101086383584, doi101093acprofoso97801985670280010001, doi101093bib52150, doi101093bioinformatics17121244, doi101093molbevmsm092, doi101093oso97801951358480010001, doi101093oxfordjournalsmolbeva040259, doi107312nei92038"
}

@article{doi101016jmar200812001,
    author = "Johansson, Tobias and Siverbo, Sven",
    title = "Why is research on management accounting change not explicitly evolutionary? Taking the next step in the conceptualisation of management accounting change",
    year = "2009",
    journal = "Management Accounting Research",
    url = "https://doi.org/10.1016/j.mar.2008.12.001",
    doi = "10.1016/j.mar.2008.12.001",
    openalex = "W1992063498",
    references = "crossref2001darwinism"
}

@article{doi101038nature07891,
    author = "Shubin, Neil H. and Tabin, Cliff and Carroll, Sean B.",
    title = "Deep homology and the origins of evolutionary novelty",
    year = "2009",
    journal = "Nature",
    url = "https://doi.org/10.1038/nature07891",
    doi = "10.1038/nature07891",
    openalex = "W2012399832",
    references = "doi101016jcell200702040, doi10103841710, doi101038nature04637, doi101126science7892602, doi102307jctvjsf433"
}

Tools and methods developed during the era of quality and optimization have shown their limitations and become inappropriate in the context of the requirements of innovation. Nowadays the need to rebuild design practices in enterprises is strongly felt both in terms of human skills and methodological expertise. In part, a way to face the innovation era's difficulties has been provided through the theory of inventive problem solving. This theory represents a significant breakthrough in driving problem statement and solving in a direction that is expressed through the idea that technical systems are driven by objective laws. A second postulate concerns the notion of contradiction, but so far only few contributions have addressed the relations between laws and contradictions. This paper, through a qualitative approach, presents a solution to this limitation and proposes a possible use of laws within the choice of the appropriate conflicting pair, prior to the use of any TRIZ solving techniques. Tests to observe the impact of the proposed approach were conducted in a French engineering ‘grande école’ during three semesters with 180 engineers. The contribution of this paper is twofold. On the one hand, there is a theoretical contribution to the theory of inventive problem solving. In addition, the proposed method offers especially TRIZ practitioners new ways for problem understanding and problem formulation.

@article{doi101111j14678691200900515x,
    author = "Cavallucci, Denis and Rousselot, François and Zanni, Cécilia",
    title = "Linking Contradictions and Laws of Engineering System Evolution within the TRIZ Framework",
    year = "2009",
    journal = "Creativity and Innovation Management",
    abstract = "Tools and methods developed during the era of quality and optimization have shown their limitations and become inappropriate in the context of the requirements of innovation. Nowadays the need to rebuild design practices in enterprises is strongly felt both in terms of human skills and methodological expertise. In part, a way to face the innovation era's difficulties has been provided through the theory of inventive problem solving. This theory represents a significant breakthrough in driving problem statement and solving in a direction that is expressed through the idea that technical systems are driven by objective laws. A second postulate concerns the notion of contradiction, but so far only few contributions have addressed the relations between laws and contradictions. This paper, through a qualitative approach, presents a solution to this limitation and proposes a possible use of laws within the choice of the appropriate conflicting pair, prior to the use of any TRIZ solving techniques. Tests to observe the impact of the proposed approach were conducted in a French engineering ‘grande école’ during three semesters with 180 engineers. The contribution of this paper is twofold. On the one hand, there is a theoretical contribution to the theory of inventive problem solving. In addition, the proposed method offers especially TRIZ practitioners new ways for problem understanding and problem formulation.",
    url = "https://doi.org/10.1111/j.1467-8691.2009.00515.x",
    doi = "10.1111/j.1467-8691.2009.00515.x",
    openalex = "W2001301510"
}

@article{openalexw2611511275,
    author = "Maddison, Wayne P. and Maddison, David R.",
    title = "Mesquite: a modular system for evolutionary analysis. Version 2.6",
    year = "2009",
    openalex = "W2611511275"
}

Comparative analysis of molecular sequence data is essential for reconstructing the evolutionary histories of species and inferring the nature and extent of selective forces shaping the evolution of genes and species. Here, we announce the release of Molecular Evolutionary Genetics Analysis version 5 (MEGA5), which is a user-friendly software for mining online databases, building sequence alignments and phylogenetic trees, and using methods of evolutionary bioinformatics in basic biology, biomedicine, and evolution. The newest addition in MEGA5 is a collection of maximum likelihood (ML) analyses for inferring evolutionary trees, selecting best-fit substitution models (nucleotide or amino acid), inferring ancestral states and sequences (along with probabilities), and estimating evolutionary rates site-by-site. In computer simulation analyses, ML tree inference algorithms in MEGA5 compared favorably with other software packages in terms of computational efficiency and the accuracy of the estimates of phylogenetic trees, substitution parameters, and rate variation among sites. The MEGA user interface has now been enhanced to be activity driven to make it easier for the use of both beginners and experienced scientists. This version of MEGA is intended for the Windows platform, and it has been configured for effective use on Mac OS X and Linux desktops. It is available free of charge from http://www.megasoftware.net.

@article{doi101093molbevmsr121,
    author = "Tamura, Koichiro and Peterson, Daniel G. and Peterson, Nora and Stecher, Glen and Nei, M and Kumar, Sudhir",
    title = "MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods",
    year = "2011",
    journal = "Molecular Biology and Evolution",
    abstract = "Comparative analysis of molecular sequence data is essential for reconstructing the evolutionary histories of species and inferring the nature and extent of selective forces shaping the evolution of genes and species. Here, we announce the release of Molecular Evolutionary Genetics Analysis version 5 (MEGA5), which is a user-friendly software for mining online databases, building sequence alignments and phylogenetic trees, and using methods of evolutionary bioinformatics in basic biology, biomedicine, and evolution. The newest addition in MEGA5 is a collection of maximum likelihood (ML) analyses for inferring evolutionary trees, selecting best-fit substitution models (nucleotide or amino acid), inferring ancestral states and sequences (along with probabilities), and estimating evolutionary rates site-by-site. In computer simulation analyses, ML tree inference algorithms in MEGA5 compared favorably with other software packages in terms of computational efficiency and the accuracy of the estimates of phylogenetic trees, substitution parameters, and rate variation among sites. The MEGA user interface has now been enhanced to be activity driven to make it easier for the use of both beginners and experienced scientists. This version of MEGA is intended for the Windows platform, and it has been configured for effective use on Mac OS X and Linux desktops. It is available free of charge from http://www.megasoftware.net.",
    url = "https://doi.org/10.1093/molbev/msr121",
    doi = "10.1093/molbev/msr121",
    openalex = "W2132632499",
    references = "doi101007bf01734359, doi101007bf02101694, doi10108010635150390235520, doi10108010635150490522304, doi101093bioinformatics149817, doi101093bioinformaticsbtl446, doi101093biomet762297, doi101093oso97801951358480010001, doi101093oxfordjournalsmolbeva040023, doi101093oxfordjournalsmolbeva040454, doi101093sysbiosyq010, doi101111j155856461985tb00420x, doi101186147121055113, openalexw3217097258"
}

We tend to see history and evolution springing from separate roots, one grounded in the human world and the other in the natural world. Human beings have, however, become probably the most powerful species shaping evolution today, and human-caused evolution in other species has probably been the most important force shaping human history. This book introduces readers to evolutionary history, a new field that unites history and biology to create a fuller understanding of the past than either can produce on its own. Evolutionary history can stimulate surprising new hypotheses for any field of history and evolutionary biology. How many art historians would have guessed that sculpture encouraged the evolution of tuskless elephants? How many biologists would have predicted that human poverty would accelerate animal evolution? How many military historians would have suspected that plant evolution would convert a counter-insurgency strategy into a rebel subsidy? With examples from around the globe, this book will help readers see the broadest patterns of history and the details of their own life in a new light.

@article{doi105860choice490841,
    title = "Evolutionary history: uniting history and biology to understand life on Earth",
    year = "2011",
    journal = "Choice Reviews Online",
    abstract = "We tend to see history and evolution springing from separate roots, one grounded in the human world and the other in the natural world. Human beings have, however, become probably the most powerful species shaping evolution today, and human-caused evolution in other species has probably been the most important force shaping human history. This book introduces readers to evolutionary history, a new field that unites history and biology to create a fuller understanding of the past than either can produce on its own. Evolutionary history can stimulate surprising new hypotheses for any field of history and evolutionary biology. How many art historians would have guessed that sculpture encouraged the evolution of tuskless elephants? How many biologists would have predicted that human poverty would accelerate animal evolution? How many military historians would have suspected that plant evolution would convert a counter-insurgency strategy into a rebel subsidy? With examples from around the globe, this book will help readers see the broadest patterns of history and the details of their own life in a new light.",
    url = "https://doi.org/10.5860/choice.49-0841",
    doi = "10.5860/choice.49-0841",
    openalex = "W632483353",
    references = "crossref2001darwinism"
}

The Molecular Evolutionary Genetics Analysis (MEGA) software has matured to contain a large collection of methods and tools of computational molecular evolution. Here, we describe new additions that make MEGA a more comprehensive tool for building timetrees of species, pathogens, and gene families using rapid relaxed-clock methods. Methods for estimating divergence times and confidence intervals are implemented to use probability densities for calibration constraints for node-dating and sequence sampling dates for tip-dating analyses. They are supported by new options for tagging sequences with spatiotemporal sampling information, an expanded interactive Node Calibrations Editor, and an extended Tree Explorer to display timetrees. Also added is a Bayesian method for estimating neutral evolutionary probabilities of alleles in a species using multispecies sequence alignments and a machine learning method to test for the autocorrelation of evolutionary rates in phylogenies. The computer memory requirements for the maximum likelihood analysis are reduced significantly through reprogramming, and the graphical user interface has been made more responsive and interactive for very big data sets. These enhancements will improve the user experience, quality of results, and the pace of biological discovery. Natively compiled graphical user interface and command-line versions of MEGA11 are available for Microsoft Windows, Linux, and macOS from www.megasoftware.net.

@article{doi101093molbevmst197,
    author = "Tamura, Koichiro and Stecher, Glen and Peterson, Daniel S. and Filipski, Alan and Kumar, Sudhir",
    title = "MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0",
    year = "2013",
    journal = "Molecular Biology and Evolution",
    abstract = "The Molecular Evolutionary Genetics Analysis (MEGA) software has matured to contain a large collection of methods and tools of computational molecular evolution. Here, we describe new additions that make MEGA a more comprehensive tool for building timetrees of species, pathogens, and gene families using rapid relaxed-clock methods. Methods for estimating divergence times and confidence intervals are implemented to use probability densities for calibration constraints for node-dating and sequence sampling dates for tip-dating analyses. They are supported by new options for tagging sequences with spatiotemporal sampling information, an expanded interactive Node Calibrations Editor, and an extended Tree Explorer to display timetrees. Also added is a Bayesian method for estimating neutral evolutionary probabilities of alleles in a species using multispecies sequence alignments and a machine learning method to test for the autocorrelation of evolutionary rates in phylogenies. The computer memory requirements for the maximum likelihood analysis are reduced significantly through reprogramming, and the graphical user interface has been made more responsive and interactive for very big data sets. These enhancements will improve the user experience, quality of results, and the pace of biological discovery. Natively compiled graphical user interface and command-line versions of MEGA11 are available for Microsoft Windows, Linux, and macOS from www.megasoftware.net.",
    url = "https://doi.org/10.1093/molbev/mst197",
    doi = "10.1093/molbev/mst197",
    openalex = "W2152207030",
    references = "doi101038scientificamerican117998, doi101073pnas1213199109, doi101093bib52150, doi101093bioinformatics102189, doi101093bioinformatics17121244, doi101093bioinformaticsbts507, doi101093molbevmsr121, doi101093oso97801951358480010001, doi101126science1211028, openalexw3217097258"
}

The terms ‘evolution’ and ‘coevolution’ are widely used in organization studies but rarely defined. Often it is unclear whether they refer to single entities or populations. When specific evolutionary processes are suggested, the labelling is often misleading. For example, in the debate over the roles of individual adaptation and competitive selection, the ‘selectionist’ position of Michael Hannan and John Freeman, which emphasizes the role of selection and stress the limits of individual firm adaptability, is often described as ‘Darwinian’ whereas opposing views that emphasize adaptability are described as ‘Lamarckian’. But these labels are not strictly dichotomous. Scholars have shown that core Darwinian principles, resulting from abstract ontological communality rather than analogy, apply to social evolution. This opens up a research agenda using the principles of generalized Darwinism and the replicator–interactor framework to help understand the evolution of organizations. Some illustrations of the conceptual value of this approach are provided, including understanding the entwinement of selection and adaptation, the nature and role of organizational routines, the place of strategic choice and the growth of organizational complexity. The framework of generalized Darwinism also helps to bridge apparently divergent perspectives in the business strategy and organizational ecology literatures.

@article{doi1011770170840613485855,
    author = "Hodgson, Geoffrey M.",
    title = "Understanding Organizational Evolution: Toward a Research Agenda using Generalized Darwinism",
    year = "2013",
    journal = "Organization Studies",
    abstract = "The terms ‘evolution’ and ‘coevolution’ are widely used in organization studies but rarely defined. Often it is unclear whether they refer to single entities or populations. When specific evolutionary processes are suggested, the labelling is often misleading. For example, in the debate over the roles of individual adaptation and competitive selection, the ‘selectionist’ position of Michael Hannan and John Freeman, which emphasizes the role of selection and stress the limits of individual firm adaptability, is often described as ‘Darwinian’ whereas opposing views that emphasize adaptability are described as ‘Lamarckian’. But these labels are not strictly dichotomous. Scholars have shown that core Darwinian principles, resulting from abstract ontological communality rather than analogy, apply to social evolution. This opens up a research agenda using the principles of generalized Darwinism and the replicator–interactor framework to help understand the evolution of organizations. Some illustrations of the conceptual value of this approach are provided, including understanding the entwinement of selection and adaptation, the nature and role of organizational routines, the place of strategic choice and the growth of organizational complexity. The framework of generalized Darwinism also helps to bridge apparently divergent perspectives in the business strategy and organizational ecology literatures.",
    url = "https://doi.org/10.1177/0170840613485855",
    doi = "10.1177/0170840613485855",
    openalex = "W2056159659",
    references = "crossref2001darwinism, doi1010160002822393921965, doi101016s004873339780234x, doi10106313067010, doi101093oso97801950926910010001, doi1023071367778, doi1023072232409, doi105962bhltitle59991, doi105962bhltitle6432, doi105962bhltitle82303, openalexw3124140110"
}

@article{doi101038nature13400,
    author = "Moroz, Leonid L. and Kocot, Kevin M. and Citarella, Mathew R. and Sohn, Dosung and Norekian, Tigran P. and Povolotskaya, Inna and Grigorenko, Anastasia P. and Dailey, Christopher A. and Berezikov, Eugène and Buckley, Katherine M. and Ptitsyn, Andrey and Reshetov, Denis A. and Mukherjee, Krishanu and Moroz, Tatiana P. and Bobkova, Yelena and Yu, Fahong and Kapitonov, Vladimir V. and Jurka, Jerzy and Bobkov, Yuri V. and Swore, Joshua J. and Girardo, David O. and Fodor, Alexander and Gusev, Fedor and Sanford, Rachel and Bruders, Rebecca and Kittler, Ellen L. W. and Mills, Claudia E. and Rast, Jonathan P. and Derelle, Romain and Solovyev, Victor and Kondrashov, Fyodor A. and Swalla, Billie J. and Sweedler, Jonathan V. and Рогаев, Е. И. and Halanych, Kenneth M. and Kohn, Andrea B.",
    title = "The ctenophore genome and the evolutionary origins of neural systems",
    year = "2014",
    journal = "Nature",
    url = "https://doi.org/10.1038/nature13400",
    doi = "10.1038/nature13400",
    openalex = "W2070443686",
    references = "doi101038nrg2303, doi101098rspb20090896, doi105860choice501469, openalexw659399033"
}

@incollection{clavien2015evolution,
    author = "Clavien, Christine",
    title = "Evolution, Society, and Ethics: Social Darwinism Versus Evolutionary Ethics",
    year = "2015",
    booktitle = "Handbook of Evolutionary Thinking in the Sciences",
    url = "https://doi.org/10.1007/978-94-017-9014-7\_34",
    doi = "10.1007/978-94-017-9014-7\_34",
    pages = "725-745"
}

Next generation sequencing transformed the field of evolutionary biology and high throughput sequencing platforms are routinely used in phylogenomic, population genomic or metagenomic studies. Here I review the recent technical advancements of third generation sequencing instruments, thereby covering nanopore sequencing and single molecule real-time (SMRT) sequencing. The output and error rates are compared with sequencing platforms of the second generation (454 pyrosequencing, Illumina and Ion Torrent). Third generation sequencers produce sequence reads in hitherto unprecedented lengths and will help to strongly increase the quality of genome assemblies. Moreover, the speed of sequencing and ease of sample preparation enables sequencing in the field. Even though the output and error rate of the new generation of sequencer remains to be improved, new possibilities for evolutionary research will open up in the near future by these new techniques.

@article{doi1010801477200020151099575,
    author = "Bleidorn, Christoph",
    title = "Third generation sequencing: technology and its potential impact on evolutionary biodiversity research",
    year = "2015",
    journal = "Systematics and Biodiversity",
    abstract = "Next generation sequencing transformed the field of evolutionary biology and high throughput sequencing platforms are routinely used in phylogenomic, population genomic or metagenomic studies. Here I review the recent technical advancements of third generation sequencing instruments, thereby covering nanopore sequencing and single molecule real-time (SMRT) sequencing. The output and error rates are compared with sequencing platforms of the second generation (454 pyrosequencing, Illumina and Ion Torrent). Third generation sequencers produce sequence reads in hitherto unprecedented lengths and will help to strongly increase the quality of genome assemblies. Moreover, the speed of sequencing and ease of sample preparation enables sequencing in the field. Even though the output and error rate of the new generation of sequencer remains to be improved, new possibilities for evolutionary research will open up in the near future by these new techniques.",
    url = "https://doi.org/10.1080/14772000.2015.1099575",
    doi = "10.1080/14772000.2015.1099575",
    openalex = "W2222342855",
    references = "doi101016jtree201503003"
}

Scientific activities take place within the structured sets of ideas and assumptions that define a field and its practices. The conceptual framework of evolutionary biology emerged with the Modern Synthesis in the early twentieth century and has since expanded into a highly successful research program to explore the processes of diversification and adaptation. Nonetheless, the ability of that framework satisfactorily to accommodate the rapid advances in developmental biology, genomics and ecology has been questioned. We review some of these arguments, focusing on literatures (evo-devo, developmental plasticity, inclusive inheritance and niche construction) whose implications for evolution can be interpreted in two ways—one that preserves the internal structure of contemporary evolutionary theory and one that points towards an alternative conceptual framework. The latter, which we label the 'extended evolutionary synthesis' (EES), retains the fundaments of evolutionary theory, but differs in its emphasis on the role of constructive processes in development and evolution, and reciprocal portrayals of causation. In the EES, developmental processes, operating through developmental bias, inclusive inheritance and niche construction, share responsibility for the direction and rate of evolution, the origin of character variation and organism-environment complementarity. We spell out the structure, core assumptions and novel predictions of the EES, and show how it can be deployed to stimulate and advance research in those fields that study or use evolutionary biology.

@article{doi101098rspb20151019,
    author = "Laland, Kevin N. and Uller, Tobias and Feldman, Marcus W. and Sterelny, Kim and Müller, Gerd B. and Moczek, Armin P. and Jablonka, Eva and Odling‐Smee, John",
    title = "The extended evolutionary synthesis: its structure, assumptions and predictions",
    year = "2015",
    journal = "Proceedings of the Royal Society B Biological Sciences",
    abstract = "Scientific activities take place within the structured sets of ideas and assumptions that define a field and its practices. The conceptual framework of evolutionary biology emerged with the Modern Synthesis in the early twentieth century and has since expanded into a highly successful research program to explore the processes of diversification and adaptation. Nonetheless, the ability of that framework satisfactorily to accommodate the rapid advances in developmental biology, genomics and ecology has been questioned. We review some of these arguments, focusing on literatures (evo-devo, developmental plasticity, inclusive inheritance and niche construction) whose implications for evolution can be interpreted in two ways—one that preserves the internal structure of contemporary evolutionary theory and one that points towards an alternative conceptual framework. The latter, which we label the 'extended evolutionary synthesis' (EES), retains the fundaments of evolutionary theory, but differs in its emphasis on the role of constructive processes in development and evolution, and reciprocal portrayals of causation. In the EES, developmental processes, operating through developmental bias, inclusive inheritance and niche construction, share responsibility for the direction and rate of evolution, the origin of character variation and organism-environment complementarity. We spell out the structure, core assumptions and novel predictions of the EES, and show how it can be deployed to stimulate and advance research in those fields that study or use evolutionary biology.",
    url = "https://doi.org/10.1098/rspb.2015.1019",
    doi = "10.1098/rspb.2015.1019",
    openalex = "W2103794982",
    references = "doi101001jama195002910300087029, doi101002jezb21081, doi101017cbo9780511621123, doi101038218525a0, doi10106313050879, doi101086346135, doi101093auk1002507, doi101093oso97801951223430010001, doi101111j155856461982tb05068x, doi101126science1113832, doi101146annureves01110170000245, doi1015159780691209418, doi1015159781400847266, doi1023071367778, doi1023072260026, doi102307jctvjsf433, doi102307jctvx5wbbh, doi105860choice364478, doi105860choice396411, doi105962bhltitle27468, doi107208chicago97802263088830010001, doi107551mitpress97802625136780010001, openalexw2080618944, openalexw227636185"
}

@article{zouaoua2015application,
    author = "Zouaoua, Dalia and Crubleau, Pascal and Choulier, Denis and Richir, Simon",
    title = "Application of Evolution Laws",
    year = "2015",
    journal = "Procedia Engineering",
    url = "https://doi.org/10.1016/j.proeng.2015.12.404",
    doi = "10.1016/j.proeng.2015.12.404",
    openalex = "W2287403478",
    pages = "922-932",
    volume = "131",
    references = "doi101016s0007850607620848, doi101111j14678691200900515x, doi101111j154058852007002764x, doi101111j15405885201100848x, doi105310220052401436, openalexw134840284, openalexw637970702"
}

The ability to interpret and reason from Tree of Life (ToL) diagrams has become a vital component of science literacy in the 21st century. This article reports on the effectiveness of a research-based curriculum, including an instructional booklet, laboratory, and lectures, to teach the fundamentals of such tree thinking in an introductory biology class for science majors. We present the results of a study involving 117 undergraduates who received either our new research-based tree-thinking curriculum or business-as-usual instruction. We found greater gains in tree-thinking abilities for the experimental instruction group than for the business-as-usual group, as measured by performance on our novel assessment instrument. This was a medium size effect. These gains were observed on an unannounced test that was administered ∼5-6 weeks after the primary instruction in tree thinking. The nature of students' postinstruction difficulties with tree thinking suggests that the critical underlying concept for acquiring expert-level competence in this area is understanding that any specific phylogenetic tree is a subset of the complete, unimaginably large ToL.

@article{doi101187cbe15060127,
    author = "Novick, Laura R. and Catley, Kefyn M.",
    title = "Fostering 21st-Century Evolutionary Reasoning: Teaching Tree Thinking to Introductory Biology Students",
    year = "2016",
    journal = "CBE—Life Sciences Education",
    abstract = "The ability to interpret and reason from Tree of Life (ToL) diagrams has become a vital component of science literacy in the 21st century. This article reports on the effectiveness of a research-based curriculum, including an instructional booklet, laboratory, and lectures, to teach the fundamentals of such tree thinking in an introductory biology class for science majors. We present the results of a study involving 117 undergraduates who received either our new research-based tree-thinking curriculum or business-as-usual instruction. We found greater gains in tree-thinking abilities for the experimental instruction group than for the business-as-usual group, as measured by performance on our novel assessment instrument. This was a medium size effect. These gains were observed on an unannounced test that was administered ∼5-6 weeks after the primary instruction in tree thinking. The nature of students' postinstruction difficulties with tree thinking suggests that the critical underlying concept for acquiring expert-level competence in this area is understanding that any specific phylogenetic tree is a subset of the complete, unimaginably large ToL.",
    url = "https://doi.org/10.1187/cbe.15-06-0127",
    doi = "10.1187/cbe.15-06-0127",
    openalex = "W2556407280",
    references = "doi101002sce20436, doi101007s1205200901227, doi101007s1205201002549, doi10118619366434613"
}

@article{doi101016jbiocon201805007,
    author = "Potter, Kevin M.",
    title = "Do United States protected areas effectively conserve forest tree rarity and evolutionary distinctiveness?",
    year = "2018",
    journal = "Biological Conservation",
    url = "https://doi.org/10.1016/j.biocon.2018.05.007",
    doi = "10.1016/j.biocon.2018.05.007",
    openalex = "W2803967095",
    references = "doi101016jtree201410002"
}

During the last two decades we have seen a revival of interest in the works of Joseph Schumpeter and "evolutionary" ideas in economics more generally. A professional society honouring Schumpeter's name has been founded, and linked to it we have had for more than fifteen years now a professional journal devoted to this stream of thought. However, it has been argued that, despite these recent developments, the link between Schumpeter's own work and the more recent contributions to evolntionary economics is in fact rather weak. This paper considers this claim.

@incollection{doi104337978178811026600008,
    author = "Fagerberg, Jan",
    title = "Schumpeter and the revival of evolutionary economics: an appraisal of the literature",
    year = "2018",
    booktitle = "Edward Elgar Publishing eBooks",
    abstract = {During the last two decades we have seen a revival of interest in the works of Joseph Schumpeter and "evolutionary" ideas in economics more generally. A professional society honouring Schumpeter's name has been founded, and linked to it we have had for more than fifteen years now a professional journal devoted to this stream of thought. However, it has been argued that, despite these recent developments, the link between Schumpeter's own work and the more recent contributions to evolntionary economics is in fact rather weak. This paper considers this claim.},
    url = "https://doi.org/10.4337/9781788110266.00008",
    doi = "10.4337/9781788110266.00008",
    openalex = "W2070153097",
    references = "crossref2001darwinism"
}

The development of the theory of Darwin from 1859 to 1926 is considered. The «cohesive ephemeral» theory of heredity, dominant at this stage, was destroying the nucleus of the Darwinian concept — the notion of natural selection as the leading factor in evolution. The results of studies of geneticists of the first decades of the 20th century also pointed to the futility of the theory of natural selection as a factor directing the process of biological evolution. Keywords: «Origin of Species»; «indefinite» hereditary variability; «certain» hereditary variability; natural selection; «conjointly ephemeral» theory of heredity; «constant-corpuscular» theory of heredity.

@article{doi107124visnykutgis161904,
    author = "Vagyn, Yu. V.",
    title = "Evolution of Darwinism. The classical stage: 1859 — 1926 years",
    year = "2018",
    journal = "Visnik ukrains kogo tovaristva genetikiv i selekcioneriv",
    abstract = "The development of the theory of Darwin from 1859 to 1926 is considered. The «cohesive ephemeral» theory of heredity, dominant at this stage, was destroying the nucleus of the Darwinian concept — the notion of natural selection as the leading factor in evolution. The results of studies of geneticists of the first decades of the 20th century also pointed to the futility of the theory of natural selection as a factor directing the process of biological evolution. Keywords: «Origin of Species»; «indefinite» hereditary variability; «certain» hereditary variability; natural selection; «conjointly ephemeral» theory of heredity; «constant-corpuscular» theory of heredity.",
    url = "https://doi.org/10.7124/visnyk.utgis.16.1.904",
    doi = "10.7124/visnyk.utgis.16.1.904",
    openalex = "W2967450105",
    references = "doi10108000033793600200111, doi1023072840896, doi105962bhltitle68064, doi107124bc0007ed"
}

Abstract Despite evolution being the central idea in modern biology, considerable variation exists in its acceptance around the globe, and reports of anti-evolutionist and creationist movements are widespread. Educators need to re-evaluate the approaches used for teaching students about evolution in order to facilitate its understanding and acceptance. A major hurdle in understanding the concepts of evolution is that humans tend to view the world in a teleological way. Learners create obstacles to understanding the concepts of evolution by ascribing purpose or intent-driven actions to animals, processes, or inanimate objects. An indispensable learning tool in the field of evolution is the evolutionary tree, as it is a direct representation of evolutionary hypotheses. The ability to read and understand this form of representation is prerequisite to fully understanding the concepts of evolution. In this work, we present issues faced when attempting to teach students to read evolutionary trees as well as troublesome diagrammatic properties that may foster teleological thinking. Further, we present teaching practices and methods that may be used to avoid the above challenges (from diagrammatic and instructional perspectives). With this work, we aim to raise awareness among educators about the different potential teleological pitfalls in the field of teaching how to read evolutionary trees, and to present different approaches for minimizing teleological reasoning and thinking in evolution education.

@article{doi101186s1205201901123,
    author = "Schramm, Thilo and Schmiemann, Philipp",
    title = "Teleological pitfalls in reading evolutionary trees and ways to avoid them",
    year = "2019",
    journal = "Evolution Education and Outreach",
    abstract = "Abstract Despite evolution being the central idea in modern biology, considerable variation exists in its acceptance around the globe, and reports of anti-evolutionist and creationist movements are widespread. Educators need to re-evaluate the approaches used for teaching students about evolution in order to facilitate its understanding and acceptance. A major hurdle in understanding the concepts of evolution is that humans tend to view the world in a teleological way. Learners create obstacles to understanding the concepts of evolution by ascribing purpose or intent-driven actions to animals, processes, or inanimate objects. An indispensable learning tool in the field of evolution is the evolutionary tree, as it is a direct representation of evolutionary hypotheses. The ability to read and understand this form of representation is prerequisite to fully understanding the concepts of evolution. In this work, we present issues faced when attempting to teach students to read evolutionary trees as well as troublesome diagrammatic properties that may foster teleological thinking. Further, we present teaching practices and methods that may be used to avoid the above challenges (from diagrammatic and instructional perspectives). With this work, we aim to raise awareness among educators about the different potential teleological pitfalls in the field of teaching how to read evolutionary trees, and to present different approaches for minimizing teleological reasoning and thinking in evolution education.",
    url = "https://doi.org/10.1186/s12052-019-0112-3",
    doi = "10.1186/s12052-019-0112-3",
    openalex = "W2990019910",
    references = "doi101007s1205201002549"
}

The process of combining Darwinism and genetics, which entered the history of biology as a synthetic theory of evolution, is considered.Key words: synthetic theory of evolution, neo-Darwinism, the concept of a biological species, population genetics, genetic polymorphism, the theory of dominance, gene drift.

@article{doi107124visnykutgis1711201,
    author = "Vagyn, Yu. V.",
    title = "Evolution of darwinism. Synthetic theory of evolutions: 1926 – 1975 years",
    year = "2019",
    journal = "Visnik ukrains kogo tovaristva genetikiv i selekcioneriv",
    abstract = "The process of combining Darwinism and genetics, which entered the history of biology as a synthetic theory of evolution, is considered.Key words: synthetic theory of evolution, neo-Darwinism, the concept of a biological species, population genetics, genetic polymorphism, the theory of dominance, gene drift.",
    url = "https://doi.org/10.7124/visnyk.utgis.17.1.1201",
    doi = "10.7124/visnyk.utgis.17.1.1201",
    openalex = "W2971981968",
    references = "doi101038149637a0, doi101093genetics16297, doi105962bhltitle27468, doi105962bhltitle61216, doi107124visnykutgis161904"
}

Evolutionary developmental biology (evo-devo) is the study of the evolution of developmental mechanisms. Here, I review some of the theories, models, and laws in evo-devo, past and present. Nineteenth-century evo-devo was dominated by recapitulation theory and archetypes. It also gave us germ layer theory, the vertebral theory of the skull, floral organs as modified leaves, and the "inverted invertebrate" theory, among others. Newer theories and models include the frameshift theory, the genetic toolkit for development, the ABC model of flower development, the developmental hourglass, the zootype, Urbilateria, and the hox code. Some of these new theories show the influence of archetypes and recapitulation. Interestingly, recent studies support the old "primordial leaf," "inverted invertebrate," and "segmented head" theories. Furthermore, von Baer's first three laws may now need to be rehabilitated, and the hourglass model modified, in view of what Abzhanov has pointed out about the maternal-zygotic transition. There are many supposed "laws" of evo-devo but I argue that these are merely generalizations about trends in particular lineages. I argue that the "body plan" is an archetype, and is often used in such a way that it lacks any scientific meaning. Looking to the future, one challenge for evo-devo will be to develop new theories and models to accommodate the wealth of new data from high-throughput sequencing, including single-cell sequencing. One step in this direction is the use of sophisticated in silico analyses, as in the "transcriptomic hourglass" models.

@article{doi101002jezb23096,
    author = "Richardson, Michael K.",
    title = "Theories, laws, and models in evo‐devo",
    year = "2021",
    journal = "Journal of Experimental Zoology Part B Molecular and Developmental Evolution",
    abstract = {Evolutionary developmental biology (evo-devo) is the study of the evolution of developmental mechanisms. Here, I review some of the theories, models, and laws in evo-devo, past and present. Nineteenth-century evo-devo was dominated by recapitulation theory and archetypes. It also gave us germ layer theory, the vertebral theory of the skull, floral organs as modified leaves, and the "inverted invertebrate" theory, among others. Newer theories and models include the frameshift theory, the genetic toolkit for development, the ABC model of flower development, the developmental hourglass, the zootype, Urbilateria, and the hox code. Some of these new theories show the influence of archetypes and recapitulation. Interestingly, recent studies support the old "primordial leaf," "inverted invertebrate," and "segmented head" theories. Furthermore, von Baer's first three laws may now need to be rehabilitated, and the hourglass model modified, in view of what Abzhanov has pointed out about the maternal-zygotic transition. There are many supposed "laws" of evo-devo but I argue that these are merely generalizations about trends in particular lineages. I argue that the "body plan" is an archetype, and is often used in such a way that it lacks any scientific meaning. Looking to the future, one challenge for evo-devo will be to develop new theories and models to accommodate the wealth of new data from high-throughput sequencing, including single-cell sequencing. One step in this direction is the use of sophisticated in silico analyses, as in the "transcriptomic hourglass" models.},
    url = "https://doi.org/10.1002/jez.b.23096",
    doi = "10.1002/jez.b.23096",
    openalex = "W3204462195",
    references = "doi101002aja1002030302, doi101002jezb23096, doi101016s0022519369800160, doi101038276565a0, doi101038353031a0, doi10109301982470440010001, doi101093auk1002507, doi1023072412825, doi1023072551371, doi105962bhltitle82303, openalexw2145250129"
}

The results of the synthesis of evolutionary genetics and developmental genetics are presented, the causes of the crisis of evolutionary genetics and ways to overcome it are explained, and the mechanism of speciation of higher organisms is explained.Keywords: new evolutionary synthesis, evolutionary genetics, genetics of ontogenesis, morphogenetic program, developmental genes.

@article{vagyn2021evolution,
    author = "Vagyn, Yu. V.",
    title = "Evolution of darwinism. A new evolutionary synthesis: combining evolutionary genetics and development genetics",
    year = "2021",
    journal = "Visnik ukrains'kogo tovaristva genetikiv i selekcioneriv",
    abstract = "The results of the synthesis of evolutionary genetics and developmental genetics are presented, the causes of the crisis of evolutionary genetics and ways to overcome it are explained, and the mechanism of speciation of higher organisms is explained.Keywords: new evolutionary synthesis, evolutionary genetics, genetics of ontogenesis, morphogenetic program, developmental genes.",
    url = "https://doi.org/10.7124/visnyk.utgis.18.1-2.1356",
    doi = "10.7124/visnyk.utgis.18.1-2.1356",
    number = "1-2",
    openalex = "W3134902110",
    pages = "70-75",
    volume = "18",
    references = "doi105860choice474406, doi105962bhltitle61216, doi107124visnykutgis161904, doi107124visnykutgis1711201"
}

genes) are used in animals to produce genetic novelties that provide adaptation to a new environment. Like development, immunity is forged by interactions with the environment, namely the microbial world. Yet, when it comes to the study of immune defence mechanisms in invertebrates, interest primarily focuses on evolutionarily conserved molecules also present in humans. Here, focusing on antiviral immunity, we argue that immune genes not conserved in humans represent an unexplored resource for the discovery of new antiviral strategies. We review recent findings on the cGAS-STING pathway and explain how cyclic dinucleotides produced by cGAS-like receptors may be used to investigate the portfolio of antiviral genes in a broad range of species. This will set the stage for evo-immuno approaches, exploiting the investment in antiviral defences made by metazoans over hundreds of millions of years of evolution. This article is part of the theme issue 'Sculpting the microbiome: how host factors determine and respond to microbial colonization'.

@article{doi101098rstb20230068,
    author = "Imler, Jean‐Luc and Cai, Hua and Meignin, Carine and Martins, Nelson",
    title = "Evolutionary immunology to explore original antiviral strategies",
    year = "2024",
    journal = "Philosophical Transactions of the Royal Society B Biological Sciences",
    abstract = "genes) are used in animals to produce genetic novelties that provide adaptation to a new environment. Like development, immunity is forged by interactions with the environment, namely the microbial world. Yet, when it comes to the study of immune defence mechanisms in invertebrates, interest primarily focuses on evolutionarily conserved molecules also present in humans. Here, focusing on antiviral immunity, we argue that immune genes not conserved in humans represent an unexplored resource for the discovery of new antiviral strategies. We review recent findings on the cGAS-STING pathway and explain how cyclic dinucleotides produced by cGAS-like receptors may be used to investigate the portfolio of antiviral genes in a broad range of species. This will set the stage for evo-immuno approaches, exploiting the investment in antiviral defences made by metazoans over hundreds of millions of years of evolution. This article is part of the theme issue 'Sculpting the microbiome: how host factors determine and respond to microbial colonization'.",
    url = "https://doi.org/10.1098/rstb.2023.0068",
    doi = "10.1098/rstb.2023.0068",
    openalex = "W4392915981",
    references = "doi101016jydbio202202007"
}

A recent American Heart Association Scientific Statement and Presidential Advisory recognized a new syndrome, the cardiovascular-kidney-metabolic syndrome. This expands our understanding of what has been called cardiorenal syndrome by incorporating the pathophysiological interrelatedness of metabolic risk factors into the previous concept of cardiorenal syndrome. Importantly, perturbation of cardiac or renal physiology combines to produce significant detrimental outcomes. The cardiorenal syndrome is a significant part of the cardiovascular-kidney-metabolic syndrome and contributes to health care cost, disability, and mortality. It is a vexing malady that has generated considerable interest. To understand the syndrome evaluation of its teleological origins is important. In life's beginning, eukaryotes acquired exocytosis for excretion, formed tubular secretory systems for clearance, and a mesenchymal nucleic acid vasoform for nutritional distribution. Those structures progressed to cardiovascular and renal systems of evolving organisms, whose migration to rivers and land imposed complex, coordinated, homeostatic roles to maintain intravascular stability. Tissue mineralization of vertebrate endoskeleton added renal calcium balance regulation, which in kidney failure results in cardiovascular calcification. Insight into cardiorenal disease can be traced to ancient Egyptian and Chinese medicine, through the Scientific Revolution, and into current insights regarding human physiology and pathophysiology. The post-World War II epidemic of cardiovascular mortality generated considerable information on cardiovascular disease, which being higher in patients with kidney disease, drew increasing health concerns. The cardiorenal syndrome was formally introduced in this setting with a focus on ultrafiltration to manage volume overload. An evolutionary review of insight into cardiorenal syndrome will help us better understand the new cardiovascular-kidney-metabolic syndrome.

@article{doi101161circheartfailure123011510,
    author = "Young, James B. and Eknoyan, Garabed",
    title = "Cardiorenal Syndrome: An Evolutionary Appraisal",
    year = "2024",
    journal = "Circulation Heart Failure",
    abstract = "A recent American Heart Association Scientific Statement and Presidential Advisory recognized a new syndrome, the cardiovascular-kidney-metabolic syndrome. This expands our understanding of what has been called cardiorenal syndrome by incorporating the pathophysiological interrelatedness of metabolic risk factors into the previous concept of cardiorenal syndrome. Importantly, perturbation of cardiac or renal physiology combines to produce significant detrimental outcomes. The cardiorenal syndrome is a significant part of the cardiovascular-kidney-metabolic syndrome and contributes to health care cost, disability, and mortality. It is a vexing malady that has generated considerable interest. To understand the syndrome evaluation of its teleological origins is important. In life's beginning, eukaryotes acquired exocytosis for excretion, formed tubular secretory systems for clearance, and a mesenchymal nucleic acid vasoform for nutritional distribution. Those structures progressed to cardiovascular and renal systems of evolving organisms, whose migration to rivers and land imposed complex, coordinated, homeostatic roles to maintain intravascular stability. Tissue mineralization of vertebrate endoskeleton added renal calcium balance regulation, which in kidney failure results in cardiovascular calcification. Insight into cardiorenal disease can be traced to ancient Egyptian and Chinese medicine, through the Scientific Revolution, and into current insights regarding human physiology and pathophysiology. The post-World War II epidemic of cardiovascular mortality generated considerable information on cardiovascular disease, which being higher in patients with kidney disease, drew increasing health concerns. The cardiorenal syndrome was formally introduced in this setting with a focus on ultrafiltration to manage volume overload. An evolutionary review of insight into cardiorenal syndrome will help us better understand the new cardiovascular-kidney-metabolic syndrome.",
    url = "https://doi.org/10.1161/circheartfailure.123.011510",
    doi = "10.1161/circheartfailure.123.011510",
    openalex = "W4397022134",
    references = "doi101007s1205200800761"
}

@incollection{doi1010079789401787062622,
    author = "Ananth, Mahesh",
    title = "Human Organisms from an Evolutionary Perspective: Its Significance for Medicine",
    year = "2025",
    url = "https://doi.org/10.1007/978-94-017-8706-2\_62-2",
    doi = "10.1007/978-94-017-8706-2\_62-2",
    openalex = "W4412102788",
    references = "doi101113jp284426"
}

@incollection{doi101007978940242252862,
    author = "Ananth, Mahesh",
    title = "Human Organisms from an Evolutionary Perspective: Its Significance for Medicine",
    year = "2025",
    url = "https://doi.org/10.1007/978-94-024-2252-8\_62",
    doi = "10.1007/978-94-024-2252-8\_62",
    openalex = "W4414726152",
    references = "doi101113jp284426"
}

Research on the biology and evolution of sex chromosomes has primarily focused on diploid XX/XY and ZW/ZZ systems. In contrast, the rise, evolution and demise of U/V systems has remained an enigma. Here we analyse genomes of nine brown algal species with different sexual systems to determine the history of their sex determination. U/V sex chromosomes emerged between 450 and 224 million years ago, when a region containing the pivotal male-determinant MIN ceased recombining. Seven ancestral genes within the sex-determining region show remarkable conservation over this vast evolutionary time, although nested inversions caused expansions of the sex locus, independently in each lineage. We evaluate whether these expansions are associated with increased morphological complexity and sexual differentiation, and show that taxonomically restricted genes evolve unexpectedly often in U and V chromosomes. We also investigate two situations in which U/V-linked regions have changed. First, we demonstrate that convergent evolution of two monoicous species occurred by ancestral males acquiring U-specific genes. Second, the Fucus dioecious system involves new sex-determining gene(s), acting upstream of formerly V-specific genes during development. Both situations have led to the demise of U and V chromosomes and erosion of their specific genomic characteristics.

@article{doi101038s4155902502838w,
    author = "Barrera‐Redondo, Josué and Lipinska, Agnieszka P. and Liu, Pengfei and Dinatale, Erica and Cossard, Guillaume and Bogaert, Kenny A. and Hoshino, Masakazu and Craig, Rory J. and Avia, Komlan and Leiria, Gonçalo and Avdievich, Elena and Liesner, Daniel and Luthringer, R. and Godfroy, Olivier and Heesch, Svenja and Nehr, Zofia and Brillet-Guéguen, Loraine and Peters, Akira F. and Hoarau, Galice and Pearson, Gareth A. and Aury, Jean‐Marc and Wincker, Patrick and Denœud, France and Cock, J. Mark and Haas, Fabian B. and Coelho, Susana M.",
    title = "Origin and evolutionary trajectories of brown algal sex chromosomes",
    year = "2025",
    journal = "Nature Ecology \& Evolution",
    abstract = "Research on the biology and evolution of sex chromosomes has primarily focused on diploid XX/XY and ZW/ZZ systems. In contrast, the rise, evolution and demise of U/V systems has remained an enigma. Here we analyse genomes of nine brown algal species with different sexual systems to determine the history of their sex determination. U/V sex chromosomes emerged between 450 and 224 million years ago, when a region containing the pivotal male-determinant MIN ceased recombining. Seven ancestral genes within the sex-determining region show remarkable conservation over this vast evolutionary time, although nested inversions caused expansions of the sex locus, independently in each lineage. We evaluate whether these expansions are associated with increased morphological complexity and sexual differentiation, and show that taxonomically restricted genes evolve unexpectedly often in U and V chromosomes. We also investigate two situations in which U/V-linked regions have changed. First, we demonstrate that convergent evolution of two monoicous species occurred by ancestral males acquiring U-specific genes. Second, the Fucus dioecious system involves new sex-determining gene(s), acting upstream of formerly V-specific genes during development. Both situations have led to the demise of U and V chromosomes and erosion of their specific genomic characteristics.",
    url = "https://doi.org/10.1038/s41559-025-02838-w",
    doi = "10.1038/s41559-025-02838-w",
    openalex = "W4413494774",
    references = "doi101038s41586024080598"
}

This review explores agency, behavior intrinsic to an organism and initiated by it, as it relates to the development of multicellular organisms and its evolution. We ask how agential behaviors contribute to and change concomitantly with evolutionary transitions from unicellularity to multicellularity, including evolution of animals from their closest unicellular antecedents. We consider the relation of organizational properties to the agency of multicellular organisms and conclude, surprisingly, that it is not as strict as it is for individual cells. The main reasons are previously unacknowledged morphogenetic inherencies of multicellular matter and the capacity of development to amplify and partition functionalities of constituent cells. These modalities generate novel phenotypic enablements that enhance the scope of agential behavior. We discuss experimental approaches to distinguish between agency and evolved, stereotypical behaviors of organisms, including purposeful actions. We argue that evolved complexities of animal development make it unsuitable for exploring single-cell-to-multicellular transformations in agency experimentally. We focus our attention instead on agency in the life cycles of social bacteria and amoebae, and in the transitions between multicellular and unicellular states in cancer. Finally, we discuss mathematical representations of incompletely specified dynamical systems and how they may be used to characterize biological autonomy and agency.

@article{doi101086735964,
    author = "Newman, Stuart A. and Benítez, Mariana and Bhat, Ramray and Glimm, Tilmann and Kumar, K. Vijay and Nanjundiah, Vidyanand and Nicholson, Daniel J. and Sarkar, Sahotra",
    title = "Agency in the Evolutionary Transition to Multicellularity",
    year = "2025",
    journal = "The Quarterly Review of Biology",
    abstract = "This review explores agency, behavior intrinsic to an organism and initiated by it, as it relates to the development of multicellular organisms and its evolution. We ask how agential behaviors contribute to and change concomitantly with evolutionary transitions from unicellularity to multicellularity, including evolution of animals from their closest unicellular antecedents. We consider the relation of organizational properties to the agency of multicellular organisms and conclude, surprisingly, that it is not as strict as it is for individual cells. The main reasons are previously unacknowledged morphogenetic inherencies of multicellular matter and the capacity of development to amplify and partition functionalities of constituent cells. These modalities generate novel phenotypic enablements that enhance the scope of agential behavior. We discuss experimental approaches to distinguish between agency and evolved, stereotypical behaviors of organisms, including purposeful actions. We argue that evolved complexities of animal development make it unsuitable for exploring single-cell-to-multicellular transformations in agency experimentally. We focus our attention instead on agency in the life cycles of social bacteria and amoebae, and in the transitions between multicellular and unicellular states in cancer. Finally, we discuss mathematical representations of incompletely specified dynamical systems and how they may be used to characterize biological autonomy and agency.",
    url = "https://doi.org/10.1086/735964",
    doi = "10.1086/735964",
    openalex = "W4410763737",
    references = "doi101007s13752024004717, doi1010179781108616751"
}