@article{doi101007bf00137351,
    author = "Gould, Stephen Jay",
    title = "Dollo on Dollo's law: Irreversibility and the status of evolutionary laws",
    year = "1970",
    journal = "Journal of the History of Biology",
    url = "https://doi.org/10.1007/bf00137351",
    doi = "10.1007/bf00137351",
    openalex = "W1971035778"
}

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

@article{doi101126science2064415217,
    author = "Raup, David M.",
    title = "Size of the Permo-Triassic Bottleneck and Its Evolutionary Implications",
    year = "1979",
    journal = "Science",
    abstract = "Rarefaction analysis of extinctions in the Late Permian indicates that as many as 96 percent of all marine species may have died out, thus forcing the marine biosphere to pass through a small bottleneck. With such severity of extinction, chance elimination of certain biologic groups would have been probable. Some of the changes in biologic composition observed at the Permo-Triassic boundary may be explained as an evolutionary founder effect that followed the bottleneck.",
    url = "https://doi.org/10.1126/science.206.4415.217",
    doi = "10.1126/science.206.4415.217",
    openalex = "W2067885793",
    references = "doi101017s0094837300002633, doi101017s0094837300004917, doi101017s0094837300005972, doi101017s0094837300006539, doi101086282541, doi101086282781, doi101098rstb19250002, doi101126science17740541065, doi101126science2034379458, doi1023071934145, doi105281zenodo16226412, valentine1978a"
}

@article{crossref1987asymmetry,
    title = "Asymmetry of lineages and the direction of evolutionary time",
    year = "1987",
    journal = "Deep Sea Research Part B. Oceanographic Literature Review",
    url = "https://doi.org/10.1016/0198-0254(87)96146-2",
    doi = "10.1016/0198-0254(87)96146-2",
    number = "12",
    openalex = "W4233080495",
    pages = "1077",
    volume = "34"
}

@article{doi101126science23648071437,
    author = "Gould, S J and Gilinsky, N L and German, R Z",
    title = "Asymmetry of lineages and the direction of evolutionary time.",
    year = "1987",
    journal = "Science (New York, N.Y.)",
    abstract = {Evolutionary time has a characteristic direction as demonstrated by the asymmetry of clade diversity diagrams in large statistical samples. Evolutionary groups generally concentrate diversity during their early histories, producing a preponderance of bottom-heavy clades among those that arise early in the history of a larger group. This pattern holds across taxonomic levels and across differences in anatomy and ecology (marine invertebrates, terrestrial mammals). The quantitative study of directionality in life's history (replacing vague, untestable, and culturally laden notions of "progress") should receive more attention from paleobiologists.},
    url = "https://pubmed.ncbi.nlm.nih.gov/17793231/",
    doi = "10.1126/science.236.4807.1437",
    openalex = "W1986740993",
    pmid = "17793231",
    references = "doi101017s009483730000508x, doi101017s0094837300008186, doi101038293435a0, doi101086627905, doi101093sysbio233305, doi101126science2064415217, doi1023072412538, doi1023072694382, openalexw2754161204, openalexw659460302"
}

@article{gould1987asymmetry,
    author = "Gould, Stephen Jay and Gilinsky, Norman L. and German, Rebecca Z.",
    title = "Asymmetry of Lineages and the Direction of Evolutionary Time",
    year = "1987",
    journal = "Science",
    abstract = {Evolutionary time has a characteristic direction as demonstrated by the asymmetry of clade diversity diagrams in large statistical samples. Evolutionary groups generally concentrate diversity during their early histories, producing a preponderance of bottom-heavy clades among those that arise early in the history of a larger group. This pattern holds across taxonomic levels and across differences in anatomy and ecology (marine invertebrates, terrestrial mammals). The quantitative study of directionality in life's history (replacing vague, untestable, and culturally laden notions of "progress") should receive more attention from paleobiologists.},
    url = "https://doi.org/10.1126/science.236.4807.1437",
    doi = "10.1126/science.236.4807.1437",
    number = "4807",
    openalex = "W1986740993",
    pages = "1437-1441",
    volume = "236",
    references = "doi101017s009483730000508x, doi101017s0094837300008022, doi101017s0094837300008186, doi101038293435a0, doi101086627905, doi101093sysbio233305, doi101126science2064415217, doi1023072412538, doi1023072694382, openalexw2754161204, openalexw659460302"
}

@misc{gould1987asymmetry1,
    author = "Gould, S. J. and Gilinsky, N. L. and German, R. Z",
    title = "Asymmetry of lineages and the directions of evolutionary time",
    year = "1987",
    howpublished = "Science, v. 236, p. 1437-1441",
    note = "talkorigins\_source = {true}; raw\_reference = {Gould, S. J., Gilinsky, N. L., and German, R. Z., 1987, Asymmetry of lineages and the directions of evolutionary time: Science, v. 236, p. 1437-1441.}"
}

@article{doi101017s009483730001263x,
    author = "Wills, Matthew A. and Briggs, Derek E. G. and Fortey, Richard A.",
    title = "Disparity as an evolutionary index: a comparison of Cambrian and Recent arthropods",
    year = "1994",
    journal = "Paleobiology",
    abstract = "Disparity is a measure of the range or significance of morphology in a given sample of organisms, as opposed to diversity, which is expressed in terms of the number (and sometimes ranking) of taxa. At present there is no agreed definition of disparity, much less any consensus on how to measure it. Two possible categories of metric are considered here, one independent of any hypothesis of relationship (phenetics), the other constrained within an evolutionary framework (cladistics). The Early Cambrian radiation was clearly a period of significant morphologic and taxonomic diversification. However, we question the interpretation of its first generation products as numerous body plans at the highest level. Four phenetic and two cladistic measures have been used to compare disparity among Cambrian arthropods with that in the living fauna. Phenetic methods assessing character-state variability and the amount of morphological attribute space occupied yield similar results for Cambrian and Recent arthropods. Assessments of disparity within a taxonomic framework rely on the identification of particular characters that delineate higher level body plans. This requires a phylogenetic interpretation, a cladistic investigation of hierarchical structure in the data. Both sets of arthropods fall within the same major clades, and within this cladistic framework the amount of character-state evolution in the two groups is comparable. None of these methods identifies markedly greater disparity among the Cambrian compared with the Recent taxa. Although measures of disparity are applied here to a consideration of the Cambrian radiation, the metrics clearly have a much wider potential for estimating macroevolutionary trends independently from existing taxonomic frameworks. Geometric morphometry is ideal for measuring morphological variety at lower taxonomic levels, but it requires the recognition of homologous landmarks in all the forms under comparison, or the identification of entire homologous structures. Conventional phenetics has much wider application as it can operate on data coded as discrete homologous character states (this facility is also a requirement of cladistics), which are a more appropriate basis for comparing disparity in markedly dissimilar forms.",
    url = "https://doi.org/10.1017/s009483730001263x",
    doi = "10.1017/s009483730001263x",
    openalex = "W2131955742",
    references = "crossref1977chapter, doi101007bf02289565, doi101007bf02289630, doi101007bf02289694, doi101017s0094837300015864, doi101093biomet5334325, doi101098rstb19810007, doi101098rstb19830020, doi101098rstb19850005, doi101111j155856461982tb05453x, doi10113719781611970319, doi101144gsjgs14940631, doi1023072288218, doi1023072346439, doi103133ofr81743, doi105281zenodo16435756, doi105860choice273873, openalexw2754161204, openalexw2944885317"
}

@article{doi101098rstb19940068,
    author = "Nee, Sean and May, Robert M. and Harvey, Paul",
    title = "The reconstructed evolutionary process",
    year = "1994",
    journal = "Philosophical Transactions of the Royal Society B Biological Sciences",
    abstract = "Phylogenies reconstructed from contemporary taxa do not contain information about lineages that have gone extinct. We derive probability models for such phylogenies, allowing real data to be compared with specified null models of evolution, and lineage birth and death rates to be estimated.",
    url = "https://doi.org/10.1098/rstb.1994.0068",
    doi = "10.1098/rstb.1994.0068",
    openalex = "W2154552181",
    references = "doi101086627905"
}

@article{doi101111j155856461994tb02211x,
    author = "McShea, Daniel W.",
    title = "MECHANISMS OF LARGE-SCALE EVOLUTIONARY TRENDS",
    year = "1994",
    journal = "Evolution",
    abstract = "Large-scale evolutionary trends may result from driving forces or from passive diffusion in bounded spaces. Such trends are persistent directional changes in higher taxa spanning significant periods of geological time; examples include the frequently cited long-term trends in size, complexity, and fitness in life as a whole, as well as trends in lesser supraspecific taxa and trends in space. In a driven trend, the distribution mean increases on account of a force (which may manifest itself as a bias in the direction of change) that acts on lineages throughout the space in which diversification occurs. In a passive system, no pervasive force or bias exists, but the mean increases because change in one direction is blocked by a boundary, or other inhomogeneity, in some limited region of the space. Two tests have been used to distinguish these trend mechanisms: (1) the test based on the behavior of the minimum; and (2) the ancestor-descendant test, based on comparisons in a random sample of ancestor-descendant pairs that lie far from any possible lower bound. For skewed distributions, a third test is introduced here: (3) the subclade test, based on the mean skewness of a sample of subclades drawn from the tail of a terminal distribution. With certain restrictions, a system is driven if the minimum increases, if increases significantly outnumber decreases among ancestor-descendant pairs, and if the mean skew of subclades is significantly positive. A passive mechanism is more difficult to demonstrate but is the more likely mechanism if decreases outnumber increases and if the mean skew of subclades is negative. Unlike the other tests, the subclade test requires no detailed phylogeny or paleontological time series, but only terminal (e.g., modern) distributions. Monte Carlo simulations of the diversification of a clade are used to show how the subclade test works. In the empirical cases examined, the three tests gave concordant results, suggesting first, that they work, and second, that the passive and driven mechanisms may correspond to natural categories of causes of large-scale trends.",
    url = "https://doi.org/10.1111/j.1558-5646.1994.tb02211.x",
    doi = "10.1111/j.1558-5646.1994.tb02211.x",
    openalex = "W1992960291",
    references = "doi101007bf00132234, doi101017s0022336000059126, doi101038365748a0, doi101111j109583121992tb00630x, doi1023072412538, doi1023073514444"
}

@article{doi101146annureves25110194001251,
    author = "Vermeij, Geerat J.",
    title = "THE EVOLUTIONARY INTERACTION AMONG SPECIES: Selection, Escalation, and Coevolution",
    year = "1994",
    journal = "Annual Review of Ecology and Systematics",
    abstract = "The hypothesis of escalation states that enemies-competitors, predators, and dangerous prey-are the most important agents of natural selection among individual organisms, and that enemy-related adaptation and responses brought about long-term evolutionary trends in the morphology, behavior, and distribution of organisms over the course of the Phanerozoic. In contrast to this top-down view of the role of organisms in determining the directions of evolution, the hypothesis of coevolution holds that two interacting species or groups of species change in response to each other. I review and evaluate these hypotheses in the light of criticisms about the existence of evolutionary trends and the role of interactions of species in evolution. Models describing the evolutionary effects organisms have on each other have been based largely on population dynamics and on cost-benefit analyses of the net outcome of interactions between species. Yet, the hypotheses of escalation and coevolution are statements about the nature, frequency, causes, and role of selection. Although these models have provided valuable insights and have forced some modifications in the hypotheses of escalation, studies seeking to distinguish between escalation and coevolution will require empirical observations and cost-benefit evaluations of the discrete events of interaction that collectively constitute organism-caused selection.",
    url = "https://doi.org/10.1146/annurev.es.25.110194.001251",
    doi = "10.1146/annurev.es.25.110194.001251",
    openalex = "W2112937332",
    references = "doi101017s0022336000059126, doi101017s0094837300011350, doi101017s0094837300012793, doi101017s0094837300013920, doi101111j155856461959tb03005x"
}

@article{doi101038374227a0,
    author = "Szathmáry, Eörs and Smith, John Maynard",
    title = "The major evolutionary transitions",
    year = "1995",
    journal = "Nature",
    url = "https://doi.org/10.1038/374227a0",
    doi = "10.1038/374227a0",
    openalex = "W2058598267",
    references = "doi10100797836427811004, doi101007bf00450633, doi101007bf00623322, doi1010160022519364900384, doi101016s0022519389801699, doi101017s0140525x00081061, doi101038371215a0, doi101111j155856461995tb04464x, doi101128mr5244524841988, doi1015159781400820108, doi1015159781400858712, doi1023072063069, doi1023072576242, doi107312rens91062, openalexw2624262714"
}

@article{doi101086419657,
    author = "Mooers, Arne Ø. and Heard, Stephen B.",
    title = "Inferring Evolutionary Process from Phylogenetic Tree Shape",
    year = "1997",
    journal = "The Quarterly Review of Biology",
    abstract = "Inferences about macroevolutionary processes have traditionally depended solely on the fossil record, but such inferences can be strengthened by also considering the shapes of the phylogenetic trees that link extant taxa. The realization that phylogenies reflect macroevolutionary processes has led to a growing literature of theoretical and comparative studies of tree shape. Two aspects of tree shape are particularly important: tree balance and the distribution of branch lenghts. We examine and evaluate recent developments in and connections between these two aspects, and suggest directions for future research. Studies of tree shape promise useful and powerful tests of macroevolutionary hypotheses. With appropriate further research, tree shape may help us detect mass extinctions and adaptive radiations, measure continuos variation in speciation and extinction rates, and associate changes in these rates with ecological or biogeographical causes. The usefulness of tree shape extends well beyond the study of macroevolution. We discuss applications to other areas of biology, including coevolution, phylogenetic inference, population biology, and developmental biology.",
    url = "https://doi.org/10.1086/419657",
    doi = "10.1086/419657",
    openalex = "W2117055771",
    references = "doi101017s009483730000508x, doi10108010292389509380518, doi101098rspb19960088, doi101126science22246281123, doi10129879780300237856, doi1023072412808"
}

@article{doi101093oxfordjournalsmolbeva025731,
    author = "Sanderson, Michael J.",
    title = "A Nonparametric Approach to Estimating Divergence Times in the Absence of Rate Constancy",
    year = "1997",
    journal = "Molecular Biology and Evolution",
    abstract = "A new method for estimating divergence times when evolutionary rates are variable across lineages is proposed. The method, called nonparametric rate smoothing (NPRS), relies on minimization of ancestor-descendant local rate changes and is motivated by the likelihood that evolutionary rates are autocorrelated in time. Fossil information pertaining to minimum and/or maximum ages of nodes in a phylogeny is incorporated into the algorithms by constrained optimization techniques. The accuracy of NPRS was examined by comparison to a clock-based maximum-likelihood method in computer simulations. NPRS provides more accurate estimates of divergence times when (1) sequence lengths are sufficiently long, (2) rates are truly nonclocklike, and (3) rates are moderately to highly autocorrelated in time. The algorithms were applied to estimate divergence times in seed plants based on data from the chloroplast rbcL gene. Both constrained and unconstrained NPRS methods tended to produce divergence time estimates more consistent with paleobotanical evidence than did clock-based estimates.",
    url = "https://doi.org/10.1093/oxfordjournals.molbev.a025731",
    doi = "10.1093/oxfordjournals.molbev.a025731",
    openalex = "W1964575260",
    references = "doi101007bf01797451, doi101126science2715248470, doi10113000917613198311503tdonag20co2"
}

@article{doi105860choice344488,
    title = "Evolutionary paleobiology",
    year = "1997",
    journal = "Choice Reviews Online",
    url = "https://doi.org/10.5860/choice.34-4488",
    doi = "10.5860/choice.34-4488",
    openalex = "W4249025931"
}

@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"
}

@article{doi101126science29054941151,
    author = "Lynch, Michael and Conery, John S.",
    title = "The Evolutionary Fate and Consequences of Duplicate Genes",
    year = "2000",
    journal = "Science",
    abstract = "Gene duplication has generally been viewed as a necessary source of material for the origin of evolutionary novelties, but it is unclear how often gene duplicates arise and how frequently they evolve new functions. Observations from the genomic databases for several eukaryotic species suggest that duplicate genes arise at a very high rate, on average 0.01 per gene per million years. Most duplicated genes experience a brief period of relaxed selection early in their history, with a moderate fraction of them evolving in an effectively neutral manner during this period. However, the vast majority of gene duplicates are silenced within a few million years, with the few survivors subsequently experiencing strong purifying selection. Although duplicate genes may only rarely evolve new functions, the stochastic silencing of such genes may play a significant role in the passive origin of new species.",
    url = "https://doi.org/10.1126/science.290.5494.1151",
    doi = "10.1126/science.290.5494.1151",
    openalex = "W2019591778",
    references = "doi101023a1006392424384, doi101038387489a0, doi101046j14390388200200356x, doi101093genetics15141531, doi101093genetics1541459, doi101093nar25173389, doi101098rspb19940058, doi101126science28253941711, doi101126science28754612204, doi101242dev1994supplement125, doi1023072412932"
}

@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"
}

@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{doi101126science1084786,
    author = "Harmon, Luke J. and Schulte, James A. and Larson, Allan and Losos, Jonathan B.",
    title = "Tempo and Mode of Evolutionary Radiation in Iguanian Lizards",
    year = "2003",
    journal = "Science",
    abstract = "Identification of general properties of evolutionary radiations has been hindered by the lack of a general statistical and phylogenetic approach applicable across diverse taxa. We present a comparative analytical framework for examining phylogenetic patterns of diversification and morphological disparity with data from four iguanian-lizard taxa that exhibit substantially different patterns of evolution. Taxa whose diversification occurred disproportionately early in their evolutionary history partition more of their morphological disparity among, rather than within, subclades. This inverse relationship between timing of diversification and morphological disparity within subclades may be a general feature that transcends the historically contingent properties of different evolutionary radiations.",
    url = "https://doi.org/10.1126/science.1084786",
    doi = "10.1126/science.1084786",
    openalex = "W2002820714",
    references = "doi101017s0094837300015864, doi101111j109583121996tb01693x, doi101146annurevecolsys281129"
}

@incollection{doi101007978366206278418,
    author = "Bown, Paul R. and Lees, Jackie A. and Young, J. R.",
    title = "Calcareous nannoplankton evolution and diversity through time",
    year = "2004",
    url = "https://doi.org/10.1007/978-3-662-06278-4\_18",
    doi = "10.1007/978-3-662-06278-4\_18",
    openalex = "W138655657",
    references = "doi1010079789401149020, doi1010160011747167900654, doi1010160012825273900925, doi1010160031018291900753, doi101016s0012825200000374, doi101017cbo9780511628948, doi101017s0094837300013178, doi1010292001pa000623, doi101093oso97801985491780010001, doi101093oxfordjournalsmolbeva026092, doi101126science1059412, doi101126science23547931156, doi101126science23648071437, doi101130spe332, doi101144gsjgs15420265, doi102110pec95040129, doi1023073515466, doi102687999013, gould1987asymmetry"
}

@article{doi101016jtree200702010,
    author = "Després, Laurence and David, Jean‐Philippe and Gallet, Christiane",
    title = "The evolutionary ecology of insect resistance to plant chemicals",
    year = "2007",
    journal = "Trends in Ecology \& Evolution",
    url = "https://doi.org/10.1016/j.tree.2007.02.010",
    doi = "10.1016/j.tree.2007.02.010",
    openalex = "W2029436323",
    references = "doi101016s0378111900005333, doi101111j13652583200400529x, doi101146annurevento47091201145121"
}

@article{doi101093bioinformaticsbtm538,
    author = "Harmon, Luke J. and Weir, Jason T. and Brock, Chad D. and Glor, Richard E. and Challenger, Wendell",
    title = "GEIGER: investigating evolutionary radiations",
    year = "2007",
    journal = "Bioinformatics",
    abstract = "This open source software is written entirely in the R language and is freely available through the Comprehensive R Archive Network (CRAN) at http://cran.r-project.org/.",
    url = "https://doi.org/10.1093/bioinformatics/btm538",
    doi = "10.1093/bioinformatics/btm538",
    openalex = "W2117368100",
    references = "doi10103844766, doi101093oso97801985052350010001, doi101111j001438202001tb00826x"
}

@article{doi101111j1365294x200703522x,
    author = "Fenberg, Phillip B. and Roy, Kaustuv",
    title = "Ecological and evolutionary consequences of size‐selective harvesting: how much do we know?",
    year = "2007",
    journal = "Molecular Ecology",
    abstract = "Size-selective harvesting, where the large individuals of a particular species are preferentially taken, is common in both marine and terrestrial habitats. Preferential removal of larger individuals of a species has been shown to have a negative effect on its demography, life history and ecology, and empirical studies are increasingly documenting such impacts. But determining whether the observed changes represent evolutionary response or phenotypic plasticity remains a challenge. In addition, the problem is not recognized in most management plans for fish and marine invertebrates that still mandate a minimum size restriction. We use examples from both aquatic and terrestrial habitats to illustrate some of the biological consequences of size-selective harvesting and discuss possible future directions of research as well as changes in management policy needed to mitigate its negative biological impacts.",
    url = "https://doi.org/10.1111/j.1365-294x.2007.03522.x",
    doi = "10.1111/j.1365-294x.2007.03522.x",
    openalex = "W2139419519",
    references = "doi101017s0022336000059126"
}

@article{doi101126science1157719,
    author = "Benton, Michael J.",
    title = "The Red Queen and the Court Jester: Species Diversity and the Role of Biotic and Abiotic Factors Through Time",
    year = "2009",
    journal = "Science",
    abstract = "Evolution may be dominated by biotic factors, as in the Red Queen model, or abiotic factors, as in the Court Jester model, or a mixture of both. The two models appear to operate predominantly over different geographic and temporal scales: Competition, predation, and other biotic factors shape ecosystems locally and over short time spans, but extrinsic factors such as climate and oceanographic and tectonic events shape larger-scale patterns regionally and globally, and through thousands and millions of years. Paleobiological studies suggest that species diversity is driven largely by abiotic factors such as climate, landscape, or food supply, and comparative phylogenetic approaches offer new insights into clade dynamics.",
    url = "https://doi.org/10.1126/science.1157719",
    doi = "10.1126/science.1157719",
    openalex = "W2092302011",
    references = "doi101017s0094837300008186, doi101073pnas092150999, doi101098rspb20080715, doi101111j14754983200600611x, doi101111j14754983200600612x, doi101111j15585646200800317x, doi101126science1130880, doi101126science1156963, doi101126science1161833, doi101126science7701342, doi1016710272463420010210172dteotr20co2"
}

@article{doi101126scienceaaa4788,
    author = "Kapheim, Karen M. and Pan, Hailin and Li, Cai and Salzberg, Steven L. and Puiu, Daniela and Magoč, Tanja and Robertson, Hugh M. and Hudson, Matthew E. and Venkat, Aarti and Fischman, Brielle J. and Hernández, Álvaro González and Yandell, Mark and Ence, Daniel and Holt, Carson and Yocum, George D. and Kemp, William P. and Bosch, Jordi and Waterhouse, Robert M. and Zdobnov, Evgeny M. and Stolle, Eckart and Kraus, Frank Bernhard and Helbing, Sophie and Moritz, Robin F. A. and Glastad, Karl M. and Hunt, Brendan G. and Goodisman, Michael A. D. and Hauser, Frank and Grimmelikhuijzen, Cornelis J.P. and Pinheiro, Daniel Guariz and Nunes, Francis Morais Franco and Soares, Michelle Prioli Miranda and Tanaka, Erica D. and Simões, Zilá Luz Paulino and Hartfelder, Klaus and Evans, Jay D. and Barribeau, Seth M. and Johnson, Reed M. and Massey, Jonathan H. and Southey, Bruce R. and Hasselmann, Martin and Hamacher, Daniel and Biewer, Matthias and Kent, Clement F. and Zayed, Amro and Blatti, Charles and Sinha, Saurabh and Johnston, J. Spencer and Hanrahan, Shawn J. and Kocher, Sarah D. and Wang, Jun and Robinson, Gene E. and Zhang, Guojie",
    title = "Genomic signatures of evolutionary transitions from solitary to group living",
    year = "2015",
    journal = "Science",
    abstract = "The evolution of eusociality is one of the major transitions in evolution, but the underlying genomic changes are unknown. We compared the genomes of 10 bee species that vary in social complexity, representing multiple independent transitions in social evolution, and report three major findings. First, many important genes show evidence of neutral evolution as a consequence of relaxed selection with increasing social complexity. Second, there is no single road map to eusociality; independent evolutionary transitions in sociality have independent genetic underpinnings. Third, though clearly independent in detail, these transitions do have similar general features, including an increase in constrained protein evolution accompanied by increases in the potential for gene regulation and decreases in diversity and abundance of transposable elements. Eusociality may arise through different mechanisms each time, but would likely always involve an increase in the complexity of gene networks.",
    url = "https://doi.org/10.1126/science.aaa4788",
    doi = "10.1126/science.aaa4788",
    openalex = "W1592395964",
    references = "doi101016jbbapap201006012"
}

@article{doi101007s1169201693890,
    author = "Gontier, Nathalie",
    title = "Guest-Editorial Introduction: Converging Evolutionary Patterns in Life and Culture",
    year = "2016",
    journal = "Evolutionary Biology",
    url = "https://doi.org/10.1007/s11692-016-9389-0",
    doi = "10.1007/s11692-016-9389-0",
    openalex = "W2531608350",
    references = "doi10100797833191504517"
}

@article{doi101111bij12746,
    author = "Lloyd, Graeme T.",
    title = "Estimating morphological diversity and tempo with discrete character-taxon matrices: implementation, challenges, progress, and future directions",
    year = "2016",
    journal = "Biological Journal of the Linnean Society",
    abstract = "Discrete character-taxon matrices are increasingly being used in an attempt to understand the pattern and tempo of morphological evolution; however, methodological sophistication and bespoke software implementations have lagged behind. In the present study, an attempt is made to provide a state-of-the-art description of methodologies and introduce a new R package (Claddis) for performing foundational disparity (morphologic diversity) and rate calculations. Simulations using its core functions show that: (1) of the two most commonly used distance metrics (Generalized Euclidean Distance and Gower's Coefficient), the latter tends to carry forward more of the true signal; (2) a novel distance metric may improve signal retention further; (3) this signal retention may come at the cost of pruning incomplete taxa from the data set; and (4) the utility of bivariate plots of ordination spaces are undermined by their frequently extremely low variances. By contrast, challenges to estimating morphologic tempo are presented qualitatively, such as how trees are time-scaled and changes are counted. Both disparity and rates deserve better time series approaches that could unlock new macroevolutionary analyses. However, these challenges need not be fatal, and several potential future solutions and directions are suggested.",
    url = "https://doi.org/10.1111/bij.12746",
    doi = "10.1111/bij.12746",
    openalex = "W2280099985",
    references = "doi101016jcub201408034, doi101073pnas1302642110, doi101093bioinformaticsbtg412, doi101093biomet5234591, doi101093sysbio204406, doi101111brv12038, doi101111j10960031200800217x, doi101111j10963642200900571x, doi101111j2041210x201100169x, doi101111j2041210x201200223x, doi101111j251761611995tb02031x, doi101111pala12142, doi101126science1252243, doi101371journalpcbi1003537, doi101666009483731999251mditer20co2, doi1018637jssv022i04, doi1023072412116, doi102992014590582006371pon20co2, openalexw3217097258, openalexw586972754"
}

@article{doi101038nature21074,
    author = "Cooney, Christopher R. and Bright, Jen A. and Capp, Elliot J. R. and Chira, Angela M. and Hughes, Emma C. and Moody, Christopher J. and Nouri, L. O. and Varley, Zoë K. and Thomas, Gavin H.",
    title = "Mega-evolutionary dynamics of the adaptive radiation of birds",
    year = "2017",
    journal = "Nature",
    url = "https://doi.org/10.1038/nature21074",
    doi = "10.1038/nature21074",
    openalex = "W2585565608",
    references = "doi10100703064746897, doi101016c20100662092, doi101016jcub201508003, doi101038nature10516, doi101038nature11631, doi101038nature15697, doi101073pnas1302642110, doi101093molbevmss075, doi1011112041210x12035, doi101111j2041210x201100169x, doi101126science1157704, doi101126science1160662, doi1018637jssv033i02, doi105860choice485062"
}

@incollection{doi101007978331972478230,
    author = "Gontier, Nathalie",
    title = "On How Epistemology and Ontology Converge Through Evolution: The Applied Evolutionary Epistemological Approach",
    year = "2018",
    booktitle = "˜The œfrontiers collection",
    url = "https://doi.org/10.1007/978-3-319-72478-2\_30",
    doi = "10.1007/978-3-319-72478-2\_30",
    openalex = "W2789395182",
    references = "doi10100797833191504517"
}

@article{doi101073pnas1907847116,
    author = "Kawahara, Akito Y. and Plotkin, David and Espeland, Marianne and Meusemann, Karen and Toussaint, Emmanuel F. A. and Donath, Alexander and Gimnich, France and Frandsen, Paul B. and Zwick, Andreas and dos Reis, Mario and Barber, Jesse R. and Peters, Ralph S. and Liu, Shanlin and Zhou, Xin and Mayer, Christoph and Podsiadłowski, Lars and Storer, Caroline and Yack, Jayne E. and Misof, Bernhard and Breinholt, Jesse W.",
    title = "Phylogenomics reveals the evolutionary timing and pattern of butterflies and moths",
    year = "2019",
    journal = "Proceedings of the National Academy of Sciences",
    abstract = "Butterflies and moths (Lepidoptera) are one of the major superradiations of insects, comprising nearly 160,000 described extant species. As herbivores, pollinators, and prey, Lepidoptera play a fundamental role in almost every terrestrial ecosystem. Lepidoptera are also indicators of environmental change and serve as models for research on mimicry and genetics. They have been central to the development of coevolutionary hypotheses, such as butterflies with flowering plants and moths’ evolutionary arms race with echolocating bats. However, these hypotheses have not been rigorously tested, because a robust lepidopteran phylogeny and timing of evolutionary novelties are lacking. To address these issues, we inferred a comprehensive phylogeny of Lepidoptera, using the largest dataset assembled for the order (2,098 orthologous protein-coding genes from transcriptomes of 186 species, representing nearly all superfamilies), and dated it with carefully evaluated synapomorphy-based fossils. The oldest members of the Lepidoptera crown group appeared in the Late Carboniferous (∼300 Ma) and fed on nonvascular land plants. Lepidoptera evolved the tube-like proboscis in the Middle Triassic (∼241 Ma), which allowed them to acquire nectar from flowering plants. This morphological innovation, along with other traits, likely promoted the extraordinary diversification of superfamily-level lepidopteran crown groups. The ancestor of butterflies was likely nocturnal, and our results indicate that butterflies became day-flying in the Late Cretaceous (∼98 Ma). Moth hearing organs arose multiple times before the evolutionary arms race between moths and bats, perhaps initially detecting a wide range of sound frequencies before being co-opted to specifically detect bat sonar. Our study provides an essential framework for future comparative studies on butterfly and moth evolution.",
    url = "https://doi.org/10.1073/pnas.1907847116",
    doi = "10.1073/pnas.1907847116",
    openalex = "W2982062771",
    references = "doi101073pnas1213621109, doi101093bioinformaticsbtu033, doi101093molbevmsm088, doi101093molbevmst010, doi101093molbevmsu300, doi101093molbevmsw260, doi101093molbevmsx281, doi101093nargkl315, doi101093sysbiosyq010, doi101098rspb20120683, doi101111evo12681, doi101111j155856461964tb01674x, doi101111j2041210x201100169x, doi101186s128590182129y"
}

@article{doi101086703055,
    author = "Huey, Raymond B. and Garland, Theodore and Turelli, Michael",
    title = "Revisiting a Key Innovation in Evolutionary Biology: Felsenstein’s “Phylogenies and the Comparative Method”",
    year = "2019",
    journal = "The American Naturalist",
    abstract = {The comparative method has long been a fundamental exploratory tool in evolutionary biology, but this venerable approach was revolutionized in 1985, when Felsenstein published "Phylogenies and the Comparative Method" in The American Naturalist. This article forced comparative biologists to start thinking phylogenetically when conducting statistical analyses of correlated trait evolution rather than simply applying conventional statistical methods that ignore evolutionary relationships. It did so by introducing a novel analytical method (phylogenetically "independent contrasts") that required a phylogenetic topology with branch lengths and that assumed a Brownian motion model of trait evolution. Independent contrasts enabled comparative biologists to avoid the statistical dilemma of nonindependence of species values, arising from shared ancestry, but came at the cost of needing a detailed phylogeny and of accepting a specific model of character change. Nevertheless, this article not only revitalized comparative biology but even encouraged studies aimed at estimating phylogenies. Felsenstein's characteristically lucid and concise statement of the problem (illustrated with powerful graphics), coupled with an oncoming flood of new molecular data and techniques for estimating phylogenies, led Felsenstein's 1985 article to become the second most cited article in the history of this journal. Here we present a personal review of comparative biology before, during, and after Joe's article. For historical context, we append a perspective written by Joe himself that describes how his article evolved, unedited transcripts of reviews of his submitted manuscript, and a guide to some nontrivial calculations. These additional materials help emphasize that the process of science does not always occur gradually or predictably.},
    url = "https://doi.org/10.1086/703055",
    doi = "10.1086/703055",
    openalex = "W2933507162",
    references = "doi101073pnas0704088104, doi101086660020, doi101086physzool67430163866, doi101093sysbiosyy031, doi101242jeb01745"
}