text:
impacts have never been examined simultaneously. Here, we analyse a global database of fossil marine animals spanning the past 500 million years, examining differential extinction with respect to multiple rarity types within each geological stage. We observe systematic differences in extinction risk over time among marine genera classified according to their rarity. Geographic range played a primary role in determining extinction, and habitat breadth a secondary role, whereas local abundance had little effect. These results suggest that current reductions in geographic range size will lead to pronounced increases in long-term extinction risk even if local populations are relatively large at present.},
URL = {http://rspb.royalsocietypublishing.org/content/279/1749/4969.abstract},
eprint = {http://rspb.royalsocietypublishing.org/content/279/1749/4969.full.pdf+html},
journal = {Proceedings of the Royal Society B: Biological Sciences}
}

@Book{Adaptation,
author = {Rose, Michael R. and Lauder, George V.},
ALTeditor = {•},
title = {Adaptation},
publisher = {Academic Press},
year = {1996},
OPTkey = {•},
OPTvolume = {•},
OPTnumber = {•},
OPTseries = {•},
OPTaddress = {•},
OPTedition = {•},
OPTmonth = {•},
OPTnote = {•},
OPTannote = {•}
}

@article{Wainwright2007,
author = {Wainwright, Peter C.},
title = {Functional Versus Morphological Diversity in Macroevolution},
journal = {Annual Review of Ecology, Evolution, and Systematics},
volume = {38},
number = {1},
pages = {381--401},
year = {2007},
doi = {10.1146/annurev.ecolsys.38.091206.095706},
URL = {http://www.annualreviews.org/doi/abs/10.1146/annurev.ecolsys.38.091206.095706},
eprint = {http://www.annualreviews.org/doi/pdf/10.1146/annurev.ecolsys.38.091206.095706}
}

@article{Baum1991,
author = {Baum, David A. and Larson, Allan},
title = {Adaptation Reviewed: A Phylogenetic Methodology for Studying Character Macroevolution},
volume = {40},
number = {1},
pages = {1--18},
year = {1991},
doi = {10.1093/sysbio/40.1.1},
abstract ={We present a phylogenetic methodology to test hypotheses of adaptation and to discriminate adaptation from alternative causal explanations of character evolution. To constitute an adaptation, a character must be shown to provide current utility to the organism and to have been generated historically through the action of natural selection for its current biological role. The criterion of current utility is applied by comparing the performance of a derived trait to that of its phylogenetically antecedent state. If the performance of a trait exceeds that of its antecedent state, it constitutes an “aptation” for its observed biological role. Alternatively, if the performance of a trait equals or falls below that of its antecedent state, it constitutes a “nonaptation” or “disaptation,” respectively. The criterion of historical genesis is applied using the concept of “selective regime,” the aggregation of organismal and environmental factors that combine to determine the expected action of natural selection on actual and potential character variation. An aptation that arose on a lineage having the same selective regime as the focal taxon constitutes an “adaptation,” whereas one that arose on a lineage having a different selective regime constitutes an “exaptation.” For nonaptations and disaptations, the criterion of historical genesis serves to determine whether the nonaptive or disaptive status arose coincident with the trait itself or secondarily through a change of selective regime. We suggest that this phylogenetic approach will help to overcome general criticisms of adaptationist studies and will serve to bridge the gap between microevolutionary and macroevolutionary studies of adaptation.},
URL = {http://sysbio.oxfordjournals.org/content/40/1/1.abstract},
eprint = {http://sysbio.oxfordjournals.org/content/40/1/1.full.pdf+html},
journal = {Systematic Biology}
}

@article{Grant2002,
author = {Grant, Peter R. and Grant, B. Rosemary},
title = {Unpredictable Evolution in a 30-Year Study of {D}arwin's Finches},
volume = {296},
number = {5568},
pages = {707--711},
year = {2002},
doi = {10.1126/science.1070315},
abstract ={Evolution can be predicted in the short term from a knowledge of selection and inheritance. However, in the long term evolution is unpredictable because environments, which determine the directions and magnitudes of selection coefficients, fluctuate unpredictably. These two features of evolution, the predictable and unpredictable, are demonstrated in a study of two populations of Darwin's finches on the Galápagos island of Daphne Major. From 1972 to 2001,Geospiza fortis (medium ground finch) and Geospiza scandens (cactus finch) changed several times in body size and two beak traits. Natural selection occurred frequently in both species and varied from unidirectional to oscillating, episodic to gradual. Hybridization occurred repeatedly though rarely, resulting in elevated phenotypic variances in G. scandens and a change in beak shape. The phenotypic states of both species at the end of the 30-year study could not have been predicted at the beginning. Continuous, long-term studies are needed to detect and interpret rare but important events and nonuniform evolutionary change.},
URL = {http://www.sciencemag.org/content/296/5568/707.abstract},
eprint = {http://www.sciencemag.org/content/296/5568/707.full.pdf},
journal = {Science}
}

@article {Siepielski2009,
author = {Siepielski, Adam M. and DiBattista, Joseph D. and Carlson, Stephanie M.},
title = {It’s about time: the temporal dynamics of phenotypic selection in the wild},
journal = {Ecology Letters},
volume = {12},
number = {11},
publisher = {Blackwell Publishing Ltd},
issn = {1461-0248},
url = {http://dx.doi.org/10.1111/j.1461-0248.2009.01381.x},
doi = {10.1111/j.1461-0248.2009.01381.x},
pages = {1261--1276},
keywords = {Adaptation, climate, demography, divergence, environmental variation, evolution, natural selection, sexual selection, temporal variation},
year = {2009},
}

@article{Siepielski2011,
author = {Siepielski, Adam M. and DiBattista, Joseph D. and Evans, Jeffrey A. and Carlson, Stephanie M.},
title = {Differences in the temporal dynamics of phenotypic selection among fitness components in the wild},
volume = {278},
number = {1711},
pages = {1572--1580},
year = {2011},
doi = {10.1098/rspb.2010.1973},
abstract ={The balance of selection acting through different fitness components (e.g. fecundity, mating success, survival) determines the potential tempo and trajectory of adaptive evolution. Yet the extent to which the temporal dynamics of phenotypic selection may vary among fitness components is poorly understood. Here, we compiled a database of 3978 linear selection coefficients from temporally replicated studies of selection in wild populations to address this question. Across studies, we find that multi-year selection through mating success and fecundity is stronger than selection through survival, but varies less in direction. We also report that selection through mating success varies more in long-term average strength than selection through either survival or fecundity. The consistency in direction and stronger long-term average strength of selection through mating success and fecundity suggests that selection through these fitness components should cause more persistent directional evolution relative to selection through survival. Similar patterns were apparent for the subset of studies that evaluated the temporal dynamics of selection on traits simultaneously using several different fitness components, but few such studies exist. Taken together, these results reveal key differences in the temporal dynamics of selection acting through different fitness components, but they also reveal important limitations in our understanding of how selection drives adaptive evolution.},
URL = {http://rspb.royalsocietypublishing.org/content/278/1711/1572.abstract},
eprint = {http://rspb.royalsocietypublishing.org/content/278/1711/1572.full.pdf+html},
journal = {Proceedings of the Royal Society B: Biological Sciences}
}

@book{Schluter2000,
	Author = {Dolph Schluter},
	Optaddress = {*},
	Optannote = {*},
	Optedition = {*},
	Optkey = {*},
	Optmonth = {*},
	Optnote = {*},
	Optnumber = {*},
	Optseries = {*},
	Optvolume = {*},
	Publisher = {Oxford University Press},
	Title = {The Ecology of Adaptive Radiation},
	Year = {2000}}

@Book{Gavrilets2004,
author = {Gavrilets, Sergey},
ALTeditor = {•},
title = {Fitness Landscapes and the Origin of Species},
publisher = {Princeton University Press},
year = {2004},
OPTkey = {•},
OPTvolume = {•},
OPTnumber = {•},
OPTseries = {•},
OPTaddress = {•},
OPTedition = {•},
OPTmonth = {•},
OPTnote = {•},
OPTannote = {•}
}

@Book{Doebeli2011,
author = {Doebeli, Michael},
ALTeditor = {•},
title = {Adaptive Diversification},
publisher = {Princeton University Press},
year = {2011},
OPTkey = {•},
OPTvolume = {•},
OPTnumber = {•},
OPTseries = {•},
OPTaddress = {•},
OPTedition = {•},
OPTmonth = {•},
OPTnote = {•},
OPTannote = {•}
}

@article{Wagner1996,
     jstor_articletype = {research-article},
     title = {Contrasting the Underlying Patterns of Active Trends in Morphologic Evolution},
     author = {Wagner, Peter J.},
     journal = {Evolution},
     jstor_issuetitle = {},
     volume = {50},
     number = {3},
     jstor_formatteddate = {Jun., 1996},
     pages = {990--1007},
     url = {http://www.jstor.org/stable/2410641},
     ISSN = {00143820},
     abstract = {Gastropod evolution during the early Paleozoic featured active trends (i.e., differential replacement of morphologies) for at least three shell characters. Selective sorting, either of individual organisms or of whole species, is an obvious mechanism for such active trends. Sorting of individuals should result in a disproportionate number of ancestor to descendant transitions being in the same direction as the trend, whereas sorting of species should result in species with particular morphologies producing more daughter species. Sorting of species can occur over long periods of time or it can be concentrated over a particular interval, such as an extinction event. Constraints on morphologic evolution also can drive trends, especially in cases where it is easier to produce a particular morphology than it is to change it. Finally, active trends can be artifacts of unrelated differential diversification within a clade (i.e., species hitchhiking), which might result from sorting of species based on phylogenetically associated characters or simply by chance. Unlike other active trends, trends attributable to species hitchhiking do not support hypotheses about selection or evolutionary constraints. From the latest Cambrian through the Silurian, gastropods show significant increases in the proportions of species with high shell torques (~= high spire height), inclined apertures, and narrow sinuses. Ancestor-descendant contrasts indicate a significant bias towards daughter species with narrower sinuses than their ancestors. This is not true for shell torque or apertural inclination. However, species with high shell torques appear constrained to produce daughter species with high shell torques. Analogous constraints do not exist for sinus width or apertural inclination. To separate the predictions of species hitchhiking from those of differential speciation and differential extinction, a bootstrapping procedure was used to simulate the range of trends that phylogenetic effects alone could generate. The simulations indicate that the trend towards species with strongly inclined apertures is indistinguishable from a phylogenetic effect. However, the simulations indicate that differential clade evolution affected the evolution of both shell torque and sinus width. The deviations between observed and expected distributions are sudden and coincide with extinction events: species with low shell torques were significantly less likely to survive the Llandeilo/Caradoc (Middle Ordovician) turnover, and species with wide sinuses were significantly less likely to survive the end-Ordovician mass extinction. However, there is not a significant association between diversification and morphology for any of the characters studied here. These results suggest that selection on individuals, evolutionary constraints, and differential survivorship over extinction events all drove trends among early gastropods.},
     language = {English},
     year = {1996},
     publisher = {Society for the Study of Evolution},
     copyright = {Copyright © 1996 Society for the Study of Evolution},
    }

@article{McShea1998,
     jstor_articletype = {research-article},
     title = {Possible Largest-Scale Trends in Organismal Evolution: Eight ``Live Hypotheses''},
     author = {McShea, Daniel W.},
     journal = {Annual Review of Ecology and Systematics},
     jstor_issuetitle = {},
     volume = {29},
     number = {},
     jstor_formatteddate = {1998},
     pages = {293--318},
     url = {http://www.jstor.org/stable/221710},
     ISSN = {00664162},
     abstract = {Historically, a great many features of organisms have been said to show a trend over the history of life, and many rationales for such trends have been proposed. Here I review eight candidates, eight "live hypotheses" that are inspiring research on largest-scale trends today: entropy, energy intensiveness, evolutionary versatility, developmental depth, structural depth, adaptedness, size, and complexity. For each, the review covers the principal arguments that have been advanced for why a trend is expected, as well as some of the empirical approaches that have been adopted. Also discussed are three conceptual matters arising in connection with trend studies: 1. Alternative bases for classifying trends: pattern versus dynamics; 2. alternative modes in which largest-scale trends have been studied: "exploratory" versus "skeptical"; and 3. evolutionary progress.},
     language = {English},
     year = {1998},
     publisher = {Annual Reviews},
     copyright = {Copyright © 1998 Annual Reviews},
    }

@article{McShea1994,
     jstor_articletype = {research-article},
     title = {Mechanisms of Large-Scale Evolutionary Trends},
     author = {McShea, Daniel W.},
     journal = {Evolution},
     jstor_issuetitle = {},
     volume = {48},
     number = {6},
     jstor_formatteddate = {Dec., 1994},
     pages = {1747--1763},
     url = {http://www.jstor.org/stable/2410505},
     ISSN = {00143820},
     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.},
     language = {English},
     year = {1994},
     publisher = {Society for the Study of Evolution},
     copyright = {Copyright © 1994 Society for the Study of Evolution},
    }

@article{Mitter1988,
     jstor_articletype = {research-article},
     title = {The Phylogenetic Study of Adaptive Zones: Has Phytophagy Promoted Insect Diversification?},
     author = {Mitter, Charles and Farrell, Brian and Wiegmann, Brian},
     journal = {The American Naturalist},
     jstor_issuetitle = {},
     volume = {132},
     number = {1},
     jstor_formatteddate = {Jul., 1988},
     pages = {107--128},
     url = {http://www.jstor.org/stable/2461756},
     ISSN = {00030147},
     abstract = {Simpson's postulate that rapid diversification follows entrance into a new "adaptive zone" is frequently invoked a posteriori for groups of unusual diversity. The postulate can be tested more rigorously by defining an adaptive zone according to ecological criteria, independent of particular groups of organisms. The adaptive-zone hypothesis predicts that if multiple lineages have invaded a new adaptive zone, they should be consistently more diverse than their (equally old) sister groups, when the latter retain the more primitive way of life. Higher-plant feeding among insects is an independently defined, repeatedly invaded adaptive zone, to which a profound acceleration of diversification rate has been attributed. We have quantified the evidence for this hypothesis by comparing sister groups and species diversity of as many phytophagous insect groups as current taxonomic evidence allows. A sign test showed significant association of diversification rate with the adoption of phytophagy. The possible artifactual bases for this trend are discussed and provisionally rejected. We discuss several possible biological explanations for the association, including models of phylogenesis either dependent on or independent of ecological role.},
     language = {English},
     year = {1988},
     publisher = {The University of Chicago Press for The American Society of Naturalists},
     copyright = {Copyright © 1988 The University of Chicago},
    }

@article{Fritz2013,
title = "Diversity in time and space: wanted dead and alive ",
journal = "Trends in Ecology \& Evolution",
volume = "",
number = "",
pages = "",
year = "2013",
note = "",
issn = "0169-5347",
doi = "http://dx.doi.org/10.1016/j.tree.2013.05.004",
url = "http://www.sciencedirect.com/science/article/pii/S0169534713001110",
author = {Susanne A. Fritz and Jan Schnitzler and Jussi T. Eronen and Christian Hof and Katrin B\"{o}hning-Gaese and Catherine H. Graham}}

@article{Adamowicz2008,
author = {Adamowicz, Sarah J. and Purvis, Andy and Wills, Matthew A.},
title = {Increasing morphological complexity in multiple parallel lineages of the Crustacea},
volume = {105},
number = {12},
pages = {4786--4791},
year = {2008},
doi = {10.1073/pnas.0709378105},
abstract ={The prospect of finding macroevolutionary trends and rules in the history of life is tremendously appealing, but very few pervasive trends have been found. Here, we demonstrate a parallel increase in the morphological complexity of most of the deep lineages within a major clade. We focus on the Crustacea, measuring the morphological differentiation of limbs. First, we show a clear trend of increasing complexity among 66 free-living, ordinal-level taxa from the Phanerozoic fossil record. We next demonstrate that this trend is pervasive, occurring in 10 or 11 of 12 matched-pair comparisons (across five morphological diversity indices) between extinct Paleozoic and related Recent taxa. This clearly differentiates the pattern from the effects of lineage sorting. Furthermore, newly appearing taxa tend to have had more types of limbs and a higher degree of limb differentiation than the contemporaneous average, whereas those going extinct showed higher-than-average limb redundancy. Patterns of contemporary species diversity partially reflect the paleontological trend. These results provide a rare demonstration of a large-scale and probably driven trend occurring across multiple independent lineages and influencing both the form and number of species through deep time and in the present day.},
URL = {http://www.pnas.org/content/105/12/4786.abstract},
eprint = {http://www.pnas.org/content/105/12/4786.full.pdf+html},
journal = {Proceedings of the National Academy of Sciences}
}

@article{Jablonski1986,
author = {Jablonski, David},
title = {Background and Mass Extinctions: The Alternation of Macroevolutionary Regimes},
volume = {231},
number = {4734},
pages = {129--133},
year = {1986},
doi = {10.1126/science.231.4734.129},
abstract ={Comparison of evolutionary patterns among Late Cretaceous marine bivalves and gastropods during times of normal, background levels of extinction and during the end-Cretaceous mass extinction indicates that mass extinctions are neither an intensification of background patterns nor an entirely random culling of the biota. During background times, traits such as planktotrophic larval development, broad geographic range of constituent species, and high species richness enhanced survivorship of species and genera. In contrast, during the, end-Cretaceous and other mass extinctions these factors were ineffectual, but broad geographic deployment of an entire lineage, regardless of the ranges of its constituent species, enhanced survivorship. Large-scale evolutionary patterns are evidently shaped by the alternation of these two macroevolutionary regimes, with rare but important mass extinctions driving shifts in the composition of the biota that have little relation to success during the background regime. Lineages or adaptations can be lost during mass extinctions for reasons unrelated to their survival values for organisms or species during background times, and long-term success would require the chance occurrence within a single lineage of sets of traits conducive to survivorship under both regimes.},
URL = {http://www.sciencemag.org/content/231/4734/129.abstract},
eprint = {http://www.sciencemag.org/content/231/4734/129.full.pdf},
journal = {Science}
}

@article{Roopnarine1999,
     jstor_articletype = {research-article},
     title = {Anagenetic Evolution, Stratophenetic Patterns, and Random Walk Models},
     author = {Roopnarine, Peter D. and Byars, Gabe and Fitzgerald, Paul},
     journal = {Paleobiology},
     jstor_issuetitle = {},
     volume = {25},
     number = {1},
     jstor_formatteddate = {Winter, 1999},
     pages = {41--57},
     url = {http://www.jstor.org/stable/2665991},
     ISSN = {00948373},
     abstract = {Previous studies have suggested that unbiased random walks may serve as appropriate null hypotheses for the detection of pattern in stratophenetic series. While numerous processes that influence the perceived temporal morphological evolution of a species may yield stratophenetic patterns that conform to the model of a random walk, use of the model as a null hypothesis raises several concerns. First, unbiased random walks are only a subset of a much larger set of random motions, including biased and fractional random walks. Some of these motions could also serve as appropriate null models for stratophenetic patterns. Second, due in part to the fractal nature of random walks, many types of time series begin to resemble random walks statistically as sampling resolution decreases. Therefore, indiscriminate support for unbiased random walks as null hypotheses of stratophenetic pattern leads inevitably to the commitment of Type II errors (incorrect failure to reject a null hypothesis). In this paper we simulate different hypothetical patterns of microevolution using various random walk models and apply the test of the null hypothesis. The frequency of Type II errors increases as stratigraphic completeness decreases, but at a currently unknown rate. Moreover, the test is insensitive to nongradual patterns of anagenesis. We also demonstrate that a previously published approach is closely related to a standard method of fractal time series analysis and represents a good qualitative test of evolutionary pattern. The statistical variation underlying this method, however, is currently unknown, and further work is required to make it a robust quantitative test.},
     language = {English},
     year = {1999},
     publisher = {Paleontological Society},
     copyright = {Copyright © 1999 Paleontological Society},
    }

@article{Marshall1990,
     jstor_articletype = {research-article},
     title = {Confidence Intervals on Stratigraphic Ranges},
     author = {Marshall, Charles R.},
     journal = {Paleobiology},
     jstor_issuetitle = {},
     volume = {16},
     number = {1},
     jstor_formatteddate = {Winter, 1990},
     pages = {1--10},
     url = {http://www.jstor.org/stable/2400927},
     ISSN = {00948373},
     abstract = {Observed stratigraphic ranges almost always underestimate true longevities. Strauss and Sadler (1987, 1989) provide a method for calculating confidence intervals on the endpoints of local stratigraphic ranges. Their method can also be applied to composite sections; confidence intervals may be placed on times of origin and extinction for entire species or lineages. Confidence interval sizes depend only on the length of the stratigraphic range and the number of fossil horizons. The technique's most important assumptions are that fossil horizons are distributed randomly and that collecting intensity has been uniform over the stratigraphic range. These assumptions are more difficult to test and less likely to be fulfilled for composite sections than for local sections. Confidence intervals give useful baseline estimates of the incompleteness of the fossil record, even if the underlying assumptions cannot be tested. Confidence intervals, which can be very large, should be calculated when the fossil record is used to assess absolute rates of molecular or morphological evolution, especially for poorly preserved groups. Confidence intervals have other functions: to determine how rich the fossil record has to be before radiometric dating errors become the dominant source of error in estimated times of origin or extinction; to predict future fossil finds; to predict which species with fossil records should be extant; and to assess phylogenetic hypotheses and taxonomic assignments.},
     language = {English},
     year = {1990},
     publisher = {Paleontological Society},
     copyright = {Copyright © 1990 Paleontological Society},
    }

@article{Marshall1994,
     jstor_articletype = {research-article},
     title = {Confidence Intervals on Stratigraphic Ranges: Partial Relaxation of the Assumption of Randomly Distributed Fossil Horizons},
     author = {Marshall, Charles R.},
     journal = {Paleobiology},
     jstor_issuetitle = {},
     volume = {20},
     number = {4},
     jstor_formatteddate = {Autumn, 1994},
     pages = {459--469},
     url = {http://www.jstor.org/stable/2401229},
     ISSN = {00948373},
     abstract = {The equations for calculating classical confidence intervals on the end points of stratigraphic ranges are based on the restrictive assumption of randomly distributed fossil finds. Herein, a method is presented for calculating confidence intervals on the end-points of stratigraphic ranges that partially relaxes this assumption: the method will work for any continuous distribution of gap sizes, not just those generated by random processes. The price paid for the generality of the new approach is twofold: (1) there are uncertainties associated with the sizes of the confidence intervals, and (2) for large confidence values (e.g., 95%) a rich fossil record is required to place upper bounds on the corresponding confidence intervals. This new method is not universal; like the method for calculating classical confidence intervals it is based on the assumption that there is no correlation between gap size and stratigraphic position. The fossil record of the Neogene Caribbean bryozoan Metrarabdotos is analyzed with the new approach. The equations developed here, like those for classical confidence intervals, should not be applied to stratigraphic ranges based on discrete sampling regimes, such as those typically established from deep-sea drilling cores, though there are exceptions to this rule.},
     language = {English},
     year = {1994},
     publisher = {Paleontological Society},
     copyright = {Copyright © 1994 Paleontological Society},
    }

@InCollection{Marshall1995,
author = {Marshall, Charles R.},
title = {Stratigraphy, the true order of species' originations and extinctions, and testing ancestor-descendant hypotheses among Caribbean bryozans},
booktitle = {New Approaches to Speciation in the Fossil Record},
OPTcrossref = {•},
OPTkey = {•},
pages = {208--236},
publisher = {Columbia University Press},
year = {1995},
editor = {Erwin, Douglas H. and Anstey, Robert L.},
OPTvolume = {•},
OPTnumber = {•},
OPTseries = {•},
OPTtype = {•},
OPTchapter = {•},
OPTaddress = {•},
OPTedition = {•},
OPTmonth = {•},
OPTnote = {•},
OPTannote = {•}
}

@Article{Marshall1997,
author = {Marshall, Charles R.},
title = {Confidence intervals on stratigraphic ranges with nonrandom distributions of fossil horizons},
journal = {Paleobiology},
year = {1997},
OPTkey = {•},
volume = {23},
OPTnumber = {•},
pages = {165--173},
OPTmonth = {•},
OPTnote = {•},
OPTannote = {•}
}

@Article{Wagner2000,
author = {Wagner, Peter J},
title = {Likelihood tests of hypothesized durations: determining and accommodatingbiasing factors},
journal = {Paleobiology},
year = {2000},
OPTkey = {•},
volume = {26},
OPTnumber = {•},
pages = {431--449},
OPTmonth = {•},
OPTnote = {•},
OPTannote = {•}
}

@article{Fujita2012,
title = "Coalescent-based species delimitation in an integrative taxonomy ",
journal = "Trends in Ecology \& Evolution ",
volume = "27",
number = "9",
pages = "480--488",
year = "2012",
note = "",
issn = "0169-5347",
doi = "http://dx.doi.org/10.1016/j.tree.2012.04.012",
url = "http://www.sciencedirect.com/science/article/pii/S0169534712001000",
author = "Matthew K. Fujita and Adam D. Leach\'{e} and Frank T. Burbrink and Jimmy A. McGuire and Craig Moritz"
}

@Article{Ricklefs2004,
author = {Ricklefs, Robert E},
title = {Cladogenesis and morphological diversification in passerine birds},
journal = {Nature},
year = {2004},
OPTkey = {•},
volume = {430},
OPTnumber = {•},
pages = {338--341},
OPTmonth = {•},
OPTnote = {•},
OPTannote = {•}
}

@InCollection{WagnerMarcot2010,
author = {Wagner, Peter J. and Marcot, Jonathan D.},
title = {Probabilistic phylogenetic inference in the fossil record: current and future applications},
booktitle = {Quantitative Methods in Paleobiology},
OPTcrossref = {•},
OPTkey = {•},
pages = {195--217},
publisher = {Paleontological Society},
year = {2010},
editor = {J Alroy and G Hunt},
OPTvolume = {•},
OPTnumber = {•},
OPTseries = {•},
OPTtype = {•},
OPTchapter = {•},
OPTaddress = {•},
OPTedition = {•},
OPTmonth = {•},
OPTnote = {•},
OPTannote = {•}
}

@article{Bokma2010,
author = {Bokma, Folmer},
title = {Time, Species, and Separating Their Effects on Trait Variance in Clades},
volume = {59},
number = {5},
pages = {602--607},
year = {2010},
doi = {10.1093/sysbio/syq029},
URL = {http://sysbio.oxfordjournals.org/content/59/5/602.short},
eprint = {http://sysbio.oxfordjournals.org/content/59/5/602.full.pdf+html},
journal = {Systematic Biology}
}

@article{Ricklefs2007,
title = "Estimating diversification rates from phylogenetic information ",
journal = "Trends in Ecology \& Evolution ",
volume = "22",
number = "11",
pages = "601--610",
year = "2007",
note = "",
issn = "0169-5347",
doi = "http://dx.doi.org/10.1016/j.tree.2007.06.013",
url = "http://www.sciencedirect.com/science/article/pii/S0169534707002698",
author = "Robert E. Ricklefs"
}

@article{Vermeij1973,
author = {Vermeij, Geerat J.},
title = {Biological Versatility and Earth History},
volume = {70},
number = {7},
pages = {1936--1938},
year = {1973},
abstract ={Examples from various plant and animal groups indicate that there has been a general increase in potential versatility of form, determined by the number and range of independently varying morphogenetic parameters, among taxa appearing at successively younger stages in the fossil record. Taxa or body plans with higher potential versatility have tended to replace less potentially versatile groups in the same or similar adaptive zone through time. Greater potential diversity allows for greater homeostasis, efficiency, and integration of structures and functions, and for an increase in size of the potential adaptive zone. In contrast, chemical versatility has generally decreased within groups from the pre-Cambrian to the Phanerozoic, partly as the result of apparent changes in the chemical environment and partly as the consequence of selection for efficiency and greater metabolic ease of handling of certain materials.},
URL = {http://www.pnas.org/content/70/7/1936.abstract},
eprint = {http://www.pnas.org/content/70/7/1936.full.pdf+html},
journal = {Proceedings of the National Academy of Sciences}
}

@article{Liem1975,
author = {Liem, Karel F. and Osse, J. W. M.},
title = {Biological Versatility, Evolution, and Food Resource Exploitation in {A}frican Cichlid Fishes},
volume = {15},
number = {2},
pages = {427--454},
year = {1975},
doi = {10.1093/icb/15.2.427},
abstract ={Increased potential versatility in form and function of the feeding apparatus of cichlid fishes has led to a prodigious proliferation in the number of possible functional solutions to an increasing variety of biological problems. Optimal utilization of every conceivable trophic resource in lacustrine environments by just one fish family, the Cichlidae, has been achieved by eruptive evolutionary radiation within the characteristically cichlid body plan producing mechanisms which partition the diverse food resources with extraordinary efficiency therefore minimizing resource sharing. There is a direct relationship between the effectiveness of trophic resource exploitation and the functional integration of the cichlid body plan in which a minimum number of adaptive compromises are necessary to evolve optimal anatomical solutions by rapidly realizable changesAnatomical data presented here reveal that cichlids possess a specific kind of mosaic in which the basic percoid jaw apparatus permits unparalleled optimal adaptations by simple morphogenetic changes while unique and dramatically diverse patterns of muscular coordination involving degrees of synchrony and extensive modulating capabilities of antagonistic muscle groups have been discovered electromyographically. At the same time the highly integrated pharyngeal jaw apparatus is sufficiently specialized providing complete freedom for the jaws to evolve into refined collecting devices.The exceptional evolutionary success of lacustrine cichlids demonstrates how rare and very specific kinds of biologically versatile morphological mosaics represent the best preadaptations for the ancestors of major new taxa. Given identical ecological conditions and temporal factors, a group of organisms possessing such rare mosaics, in which optimal biological versatility is realizable by simple evolutionary mechanisms, will dominate newly formed environments to the detriment of taxa not so endowed.},
URL = {http://icb.oxfordjournals.org/content/15/2/427.abstract},
eprint = {http://icb.oxfordjournals.org/content/15/2/427.full.pdf+html},
journal = {American Zoologist}
}

@article {Martin2011,
author = {Martin, Christopher H. and Wainwright, Peter C.},
title = {Trophic novelty is linked to exceptional rates of morphological diversification in two adaptive radiations of \textit{Cyprinodon} pupfish},
journal = {Evolution},
volume = {65},
number = {8},
publisher = {Blackwell Publishing Inc},
issn = {1558-5646},
url = {http://dx.doi.org/10.1111/j.1558-5646.2011.01294.x},
doi = {10.1111/j.1558-5646.2011.01294.x},
pages = {2197--2212},
keywords = {Brownian motion, comparative method, disparity, divergent selection, ecological speciation, lepidophagy},
year = {2011},
}

@Article{Wagner2001,
author = {Wagner, Peter J.},
title = {Rate heterogeneity in shell character evolution among lophospiroid gastropods},
journal = {Paleobiology},
year = {2001},
OPTkey = {•},
volume = {27},
OPTnumber = {•},
pages = {290--310},
OPTmonth = {•},
OPTnote = {•},
OPTannote = {•}
}

@article{Hull1980,
     jstor_articletype = {research-article},
     title = {Individuality and Selection},
     author = {Hull, David L.},
     journal = {Annual Review of Ecology and Systematics},
     jstor_issuetitle = {},
     volume = {11},
     number = {},
     jstor_formatteddate = {1980},
     pages = {311--332},
     url = {http://www.jstor.org/stable/2096911},
     ISSN = {00664162},
     abstract = {},
     language = {English},
     year = {1980},
     publisher = {Annual Reviews},
     copyright = {Copyright © 1980 Annual Reviews},
    }

@article{Alroy2008,
author = {Alroy, John},
title = {Dynamics of origination and extinction in the marine fossil record},
volume = {105},
number = {Supplement 1},
pages = {11536--11542},
year = {2008},
doi = {10.1073/pnas.0802597105},
abstract ={The discipline-wide effort to database the fossil record at the occurrence level has made it possible to estimate marine invertebrate extinction and origination rates with much greater accuracy. The new data show that two biotic mechanisms have hastened recoveries from mass extinctions and confined diversity to a relatively narrow range over the past 500 million years (Myr). First, a drop in diversity of any size correlates with low extinction rates immediately afterward, so much so that extinction would almost come to a halt if diversity dropped by 90%. Second, very high extinction rates are followed by equally high origination rates. The two relationships predict that the rebound from the current mass extinction will take at least 10 Myr, and perhaps 40 Myr if it rivals the Permo-Triassic catastrophe. Regardless, any large event will result in a dramatic ecological and taxonomic restructuring of the biosphere. The data also confirm that extinction and origination rates both declined through the Phanerozoic and that several extinctions in addition to the Permo-Triassic event were particularly severe. However, the trend may be driven by taxonomic biases and the rates vary in accord with a simple log normal distribution, so there is no sharp distinction between background and mass extinctions. Furthermore, the lack of any significant autocorrelation in the data is inconsistent with macroevolutionary theories of periodicity or self-organized criticality.},
URL = {http://www.pnas.org/content/105/suppl.1/11536.abstract},
eprint = {http://www.pnas.org/content/105/suppl.1/11536.full.pdf+html},
journal = {Proceedings of the National Academy of Sciences}
}

@article{Rabosky2009,
   author = {Rabosky, D. L.},
   title = {Ecological limits and diversification rate: alternative paradigms to explain the variation in species richness among clades and regions},
   journal = {Ecology Letters},
   volume = {12},
   number = {8},
   pages = {735--743},
   abstract = {Diversification rate is one of the most important metrics in macroecological and macroevolutionary studies. Here I demonstrate that diversification analyses can be misleading when researchers assume that diversity increases unbounded through time, as is typical in molecular phylogenetic studies. If clade diversity is regulated by ecological factors, then species richness may be independent of clade age and it may not be possible to infer the rate at which diversity arose. This has substantial consequences for the interpretation of many studies that have contrasted rates of diversification among clades and regions. Often, it is possible to estimate the total diversification experienced by a clade but not diversification rate itself. I show that the evidence for ecological limits on diversity in higher taxa is widespread. Finally, I explore the implications of ecological limits for a variety of ecological and evolutionary questions that involve inferences about speciation and extinction rates from phylogenetic data.},
   year = {2009}
}

@article{Rabosky2008,
   author = {Rabosky, D. L. and Lovette, I. J.},
   title = {Explosive evolutionary radiations: Decreasing speciation or increasing extinction through time?},
   journal = {Evolution},
   volume = {62},
   number = {8},
   pages = {1866--1875},
   abstract = {A common pattern in time-calibrated molecular phylogenies is a signal of rapid diversification early in the history of a radiation. Because the net rate of diversification is the difference between speciation and extinction rates, such "explosive-early" diversification could result either from temporally declining speciation rates or from increasing extinction rates through time. Distinguishing between these alternatives is challenging but important, because these processes likely result from different ecological drivers of diversification. Here we develop a method for estimating speciation and extinction rates that vary continuously through time. By applying this approach to real phylogenies with explosive-early diversification and by modeling features of lineage-accumulation curves under both declining speciation and increasing extinction scenarios, we show that a signal of explosive-early diversification in phylogenies of extant taxa cannot result from increasing extinction and can only be explained by temporally declining speciation rates. Moreover, whenever extinction rates are high, "explosive early" patterns become unobservable, because high extinction quickly erases the signature of even large declines in speciation rates. Although extinction may obscure patterns of evolutionary diversification, these results show that decreasing speciation is often distinguishable from increasing extinction in the numerous molecular phylogenies of radiations that retain a preponderance of early lineages.},
   year = {2008}
}

@article{RaboskyGlor2010,
author = {Rabosky, Daniel L. and Glor, Richard E.},
title = {Equilibrium speciation dynamics in a model adaptive radiation of island lizards},
volume = {107},
number = {51},
pages = {22178--22183},
year = {2010},
doi = {10.1073/pnas.1007606107},
abstract ={The relative importance of equilibrium and nonequilibrium processes in shaping patterns of species richness is one of the most fundamental questions in biodiversity studies. If equilibrium processes predominate, then ecological interactions presumably limit species diversity, potentially through diversity dependence of immigration, speciation, and extinction rates. Alternatively, species richness may be limited by the rate at which diversity arises or by the amount of time available for diversification. These latter explanations constitute nonequilibrium processes and can apply only to biotas that are unsaturated or far from diversity equilibria. Recent studies have challenged whether equilibrium models apply to biotas assembled through in situ speciation, as this process may be too slow to achieve steady-state diversities. Here we demonstrate that speciation rates in replicate Caribbean lizard radiations have undergone parallel declines to equilibrium conditions on three of four major islands. Our results suggest that feedback between total island diversity and per-capita speciation rates scales inversely with island area, with proportionately greater declines occurring on smaller islands. These results are consistent with strong ecological controls on species richness and suggest that the iconic adaptive radiation of Caribbean anoles may have reached an endpoint.},
URL = {http://www.pnas.org/content/107/51/22178.abstract},
eprint = {http://www.pnas.org/content/107/51/22178.full.pdf+html},
journal = {Proceedings of the National Academy of Sciences}
}

@article{Beaulieu2013,
author = {Beaulieu, Jeremy M. and O'Meara, Brian C. and Donoghue, Michael J.},
title = {Identifying Hidden Rate Changes in the Evolution of a Binary Morphological Character: The Evolution of Plant Habit in Campanulid Angiosperms},
year = {2013},
doi = {10.1093/sysbio/syt034},
abstract ={The growth of phylogenetic trees in scope and in size is promising from the standpoint of understanding a wide variety of evolutionary patterns and processes. With trees comprised of larger, older, and globally distributed clades, it is likely that the lability of a binary character will differ significantly among lineages, which could lead to errors in estimating transition rates and the associated inference of ancestral states. Here we develop and implement a new method for identifying different rates of evolution in a binary character along different branches of a phylogeny. We illustrate this approach by exploring the evolution of growth habit in Campanulidae, a flowering plant clade containing some 35,000 species. The distribution of woody versus herbaceous species calls into question the use of traditional models of binary character evolution. The recognition and accommodation of changes in the rate of growth form evolution in different lineages demonstrates, for the first time, a robust picture of growth form evolution across a very large, very old, and very widespread flowering plant clade. [Binary character; Campanulidae; comparative methods; flowering plants; growth habit; herbaceous; Hidden rates model; woody.]},
URL = {http://sysbio.oxfordjournals.org/content/early/2013/06/11/sysbio.syt034.abstract},
eprint = {http://sysbio.oxfordjournals.org/content/early/2013/06/11/sysbio.syt034.full.pdf+html},
journal = {Systematic Biology}
}

@article{Etienne2012AmNat,
	Author = {Etienne, R. S. and Haegeman, B.},
	Date-Added = {2012-11-12 00:04:41 -0500},
	Date-Modified = {2012-11-12 00:06:42 -0500},
	Journal = {The American Naturalist},
	Number = {4},
	Pages = {E75--E89},
	Title = {A conceptual and statistical framework for adaptive radiations with a key role for diversity dependence},
	Volume = {180},
	Year = {2012}}

@article{Etienne2012,
author = {Etienne, Rampal S. and Haegeman, Bart and Stadler, Tanja and Aze, Tracy and Pearson, Paul N. and Purvis, Andy and Phillimore, Albert B.},
title = {Diversity-dependence brings molecular phylogenies closer to agreement with the fossil record},
volume = {279},
number = {1732},
pages = {1300--1309},
year = {2012},
doi = {10.1098/rspb.2011.1439},
abstract ={The branching times of molecular phylogenies allow us to infer speciation and extinction dynamics even when fossils are absent. Troublingly, phylogenetic approaches usually return estimates of zero extinction, conflicting with fossil evidence. Phylogenies and fossils do agree, however, that there are often limits to diversity. Here, we present a general approach to evaluate the likelihood of a phylogeny under a model that accommodates diversity-dependence and extinction. We find, by likelihood maximization, that extinction is estimated most precisely if the rate of increase in the number of lineages in the phylogeny saturates towards the present or first decreases and then increases. We demonstrate the utility and limits of our approach by applying it to the phylogenies for two cases where a fossil record exists (Cetacea and Cenozoic macroperforate planktonic foraminifera) and to three radiations lacking fossil evidence (Dendroica, Plethodon and Heliconius). We propose that the diversity-dependence model with extinction be used as the standard model for macro-evolutionary dynamics because of its biological realism and flexibility.},
URL = {http://rspb.royalsocietypublishing.org/content/279/1732/1300.abstract},
eprint = {http://rspb.royalsocietypublishing.org/content/279/1732/1300.full.pdf+html},
journal = {Proceedings of the Royal Society B: Biological Sciences}
}

@article{Alfaro2009,
author = {Alfaro, M E and Santini, F and Brock, C and Alamillo, H and Dornburg, A and Rabosky, D L and Carnevale, G and Harmon, L J},
title = {Nine exceptional radiations plus high turnover
explain species diversity in jawed vertebrates},
journal = {Proceedings of the National Academy of Sciences},
year = {2009},
OPTkey = {•},
volume = {106},
number = {32},
pages = {13410--13414},
OPTmonth = {•},
OPTnote = {•},
OPTannote = {•}
}

@article{PhillimorePrice2008,
    author = {Phillimore, Albert B AND Price, Trevor D},
    journal = {PLoS Biol},
    publisher = {Public Library of Science},
    title = {Density-Dependent Cladogenesis in Birds},
    year = {2008},
    month = {03},
    volume = {6},
    url = {http://dx.doi.org/10.1371%2Fjournal.pbio.0060071},
    pages = {e71},
    abstract = {
        <p>Molecular evidence provides strong evidence that speciation rates slow down through time.</p>
      },
    number = {3},
    doi = {10.1371/journal.pbio.0060071}
}

@article{McPeek2008,
     jstor_articletype = {research-article},
     title = {The Ecological Dynamics of Clade Diversification and Community Assembly},
     author = {Mark A. McPeek},
     journal = {The American Naturalist},
     jstor_issuetitle = {},
     volume = {172},
     number = {6},
     jstor_formatteddate = {December 2008},
     pages = {E270--E284},
     url = {http://www.jstor.org/stable/10.1086/593137},
     ISSN = {00030147},
     abstract = {Abstract: Clades diversify in an ecological context, but most macroevolutionary models do not directly encapsulate ecological mechanisms that influence speciation and extinction. A data set of 245 chordate, arthropod, mollusk, and magnoliophyte phylogenies had a majority of clades that showed rapid lineage accumulation early with a slowing more recently, whereas a small but significant minority showed accelerated lineage accumulation in their recent histories. Previous analyses have demonstrated that macroevolutionary birth‐death models can replicate the pattern of slowing lineage accumulation only by a strong decrease in speciation rate with increasing species richness and extinction rate held extremely low or absent. In contrast, the metacommunity model presented here could generate the full range of patterns seen in the real phylogenies by simply manipulating the degree of ecological differentiation of new species at the time of speciation. Specifically, the metacommunity model predicts that clades showing decelerating lineage accumulation rates are those that have diversified by ecological modes of speciation, whereas clades showing accelerating lineage accumulation rates are those that have diversified primarily by modes of speciation that generate little or no ecological diversification. A number of testable predictions that integrate data from molecular systematics, community ecology, and biogeography are also discussed.},
     language = {English},
     year = {2008},
     publisher = {The University of Chicago Press for The American Society of Naturalists},
     copyright = {Copyright © 2008 The University of Chicago},
    }

@article{Rabosky2007,
author = {Rabosky, Daniel L and Donnellan, Stephen C and Talaba, Amanda L and Lovette, Irby J},
title = {Exceptional among-lineage variation in diversification rates during the radiation of {A}ustralia's most diverse vertebrate clade},
volume = {274},
number = {1628},
pages = {2915--2923},
year = {2007},
doi = {10.1098/rspb.2007.0924},
abstract ={The disparity in species richness among groups of organisms is one of the most pervasive features of life on earth. A number of studies have addressed this pattern across higher taxa (e.g. ‘beetles’), but we know much less about the generality and causal basis of the variation in diversity within evolutionary radiations at lower taxonomic scales. Here, we address the causes of variation in species richness among major lineages of Australia's most diverse vertebrate radiation, a clade of at least 232 species of scincid lizards. We use new mitochondrial and nuclear intron DNA sequences to test the extent of diversification rate variation in this group. We present an improved likelihood-based method for estimating per-lineage diversification rates from combined phylogenetic and taxonomic (species richness) data, and use the method in a hypothesis-testing framework to localize diversification rate shifts on phylogenetic trees. We soundly reject homogeneity of diversification rates among members of this radiation, and find evidence for a dramatic rate increase in the common ancestor of the genera Ctenotus and Lerista. Our results suggest that the evolution of traits associated with climate tolerance may have had a role in shaping patterns of diversity in this group.},
URL = {http://rspb.royalsocietypublishing.org/content/274/1628/2915.abstract},
eprint = {http://rspb.royalsocietypublishing.org/content/274/1628/2915.full.pdf+html},
journal = {Proceedings of the Royal Society B: Biological Sciences}
}

@article{Sepkoski1984,
     jstor_articletype = {research-article},
     title = {A Kinetic Model of Phanerozoic Taxonomic Diversity. III. Post-Paleozoic Families and Mass Extinctions},
     author = {Sepkoski, J. John Jr.},
     journal = {Paleobiology},
     jstor_issuetitle = {},
     volume = {10},
     number = {2},
     jstor_formatteddate = {Spring, 1984},
     pages = {246--267},
     url = {http://www.jstor.org/stable/2400399},
     ISSN = {00948373},
     abstract = {A three-phase kinetic model with time-specific perturbations is used to describe large-scale patterns in the diversification of Phanerozoic marine families. The basic model assumes that the Cambrian, Paleozoic, and Modern evolutionary faunas each diversified logistically as a consequence of early exponential growth and of later slowing of growth as the ecosystems became filled; it also assumes interaction among the evolutionary faunas such that expansion of the combined diversities of all three faunas above any single fauna's equilibrium caused that fauna's diversity to begin to decline. This basic model adequately describes the diversification of the evolutionary faunas through the Paleozoic Era as well as the asymmetrical rise and fall of background extinction rates through the entire Phanerozoic. Declines in diversity and changes in faunal dominance associated with mass extinctions can be accommodated in the model with short-term accelerations in extinction rates or declines in equilibria. Such accelerations, or perturbations, cause diversity to decline exponentially and then to rebound sigmoidally following release. The amount of decline is dependent on the magnitude and duration of the perturbation, the timing of the perturbation with respect to the diversification of the system, and the system's initial per-taxon rates of diversification and turnover. When applied to the three-phase model, such perturbations describe the changes in diversity and faunal dominance during and after major mass extinctions, the long-term rise in total diversity following the Late Permian and Norian mass extinctions, and the peculiar diversification and then decline of the remnants of the Paleozoic fauna during the Mesozoic and Cenozoic Eras. The good fit of this model to data on Phanerozoic familial diversity suggests that many of the large-scale patterns of diversification seen in the marine fossil record of animal families are simple consequences of nonlinear interrelationships among a small number of parameters that are intrinsic to the evolutionary faunas and are largely (but not completely) invariant through time.},
     language = {English},
     year = {1984},
     publisher = {Paleontological Society},
     copyright = {Copyright © 1984 Paleontological Society},
    }

@article{Roy1996,
     jstor_articletype = {research-article},
     title = {The Roles of Mass Extinction and Biotic Interaction in Large-Scale Replacements: A Reexamination Using the Fossil Record of Stromboidean Gastropods},
     author = {Roy, Kaustuv},
     journal = {Paleobiology},
     jstor_issuetitle = {},
     volume = {22},
     number = {3},
     jstor_formatteddate = {Summer, 1996},
     pages = {436--452},
     url = {http://www.jstor.org/stable/2401099},
     ISSN = {00948373},
     abstract = {The macroevolutionary processes underlying large-scale biotic replacements are still poorly understood. Opinion remains divided regarding the roles of mass extinction, biotic interaction, and environmental perturbations in these replacement events. Previous attempts to test replacement hypotheses have largely focused on taxonomic diversity patterns. Taxonomic data alone, however, provide little insight about ecological interactions and hence other approaches are needed to understand mechanics of biotic replacements. Here I propose a conceptual model of replacement based on predation-mediated biotic interactions, and attempt a test using analysis of the Cenozoic replacement of the gastropod family Aporrhaidae by a closely related group, the Strombidae. Taxonomic, morphologic, and geographic data analyzed in this study all suggest a replacement of aporrhaids by strombids following the end-Cretaceous mass extinction. While most of the taxonomic replacement was associated with a mass extinction, some replacement also occurred during background times and was mediated by higher origination rates in strombids rather than by higher extinction rates in aporrhaids. Morphologically, the replacement was largely confined to the portion of the morphospace unaffected by the end-Cretaceous extinction. At a global scale, the geographic overlap between the two groups declined through the Cenozoic, reflecting increasing restriction of aporrhaids to colder, temperate waters while strombids flourished in the tropics. However, at a finer geographic scale a more mosaic pattern of replacement is evident and coincides with Eocene and Oligocene climatic fluctuations. The results of this study suggest that mass extinction, long-term biotic interaction, and environmental change can all play significant roles in biotic replacements. Since the relative importance of each factor would vary from one event to another, an understanding of the general nature of large-scale biotic replacements requires a knowledge of the relative intensities of each of these processes.},
     language = {English},
     year = {1996},
     publisher = {Paleontological Society},
     copyright = {Copyright © 1996 Paleontological Society},
    }

@article{VanValen1975,
     jstor_articletype = {research-article},
     title = {Group Selection, Sex, and Fossils},
     author = {Van Valen, Leigh},
     journal = {Evolution},
     jstor_issuetitle = {},
     volume = {29},
     number = {1},
     jstor_formatteddate = {Mar., 1975},
     pages = {87--94},
     url = {http://www.jstor.org/stable/2407143},
     ISSN = {00143820},
     abstract = {The loss of sex and other recurrent unidirectional evolutionary trends can be treated as a simple equilibrium balanced by group selection. Genera of large mammals and large foraminiferans have a selective disadvantage of 0.02 to 0.05 per million years. The components of this selection act in opposite directions and in each case are much larger than the total selection, suggesting that most interspecific competition is with organisms of rather similar size. A related conjecture is disproved. Group selection is an important cause of evolution, including that of man.},
     language = {English},
     year = {1975},
     publisher = {Society for the Study of Evolution},
     copyright = {Copyright © 1975 Society for the Study of Evolution},
    }

@Article{Eble2000,
author = {Eble, G. J.},
title = {Contrasting evolutionary flexibility in sister groups: disparity and diversity in Mesozoic atelostomate echinoids},
journal = {Paleobiology},
year = {2000},
OPTkey = {•},
volume = {26},
OPTnumber = {•},
pages = {56--79},
OPTmonth = {•},
OPTnote = {•},
OPTannote = {•}
}

@Article{Sepkoski2000,
author = {Sepkoski, J. J. Jr. and McKinney, F.M. and Lidgard, S.},
title = {Competitive displacement among
post-Paleozoic cyclostome and cheilostome bryozoans},
journal = {Paleobiology},
year = {2000},
OPTkey = {•},
volume = {26},
OPTnumber = {•},
pages = {7-18},
OPTmonth = {•},
OPTnote = {•},
OPTannote = {•}
}

@Book{Vermeij1987,
author = {Vermeij, Geerat J.},
ALTeditor = {•},
title = {Evolution and Escalation},
publisher = {Princeton University Press},
year = {1987},
OPTkey = {•},
OPTvolume = {•},
OPTnumber = {•},
OPTseries = {•},
OPTaddress = {•},
OPTedition = {•},
OPTmonth = {•},
OPTnote = {•},
OPTannote = {•}
}

@article{Eo2010,
author = {Eo, Soo Hyung and DeWoody, J. Andrew},
title = {Evolutionary rates of mitochondrial genomes correspond to diversification rates and to contemporary species richness in birds and reptiles},
volume = {277},
number = {1700},
pages = {3587--3592},
year = {2010},
doi = {10.1098/rspb.2010.0965},
abstract ={Rates of biological diversification should ultimately correspond to rates of genome evolution. Recent studies have compared diversification rates with phylogenetic branch lengths, but incomplete phylogenies hamper such analyses for many taxa. Herein, we use pairwise comparisons of confamilial sauropsid (bird and reptile) mitochondrial DNA (mtDNA) genome sequences to estimate substitution rates. These molecular evolutionary rates are considered in light of the age and species richness of each taxonomic family, using a random-walk speciation–extinction process to estimate rates of diversification. We find the molecular clock ticks at disparate rates in different families and at different genes. For example, evolutionary rates are relatively fast in snakes and lizards, intermediate in crocodilians and slow in turtles and birds. There was also rate variation across genes, where non-synonymous substitution rates were fastest at ATP8 and slowest at CO3. Family-by-gene interactions were significant, indicating that local clocks vary substantially among sauropsids. Most importantly, we find evidence that mitochondrial genome evolutionary rates are positively correlated with speciation rates and with contemporary species richness. Nuclear sequences are poorly represented among reptiles, but the correlation between rates of molecular evolution and species diversification also extends to 18 avian nuclear genes we tested. Thus, the nuclear data buttress our mtDNA findings.},
URL = {http://rspb.royalsocietypublishing.org/content/277/1700/3587.abstract},
eprint = {http://rspb.royalsocietypublishing.org/content/277/1700/3587.full.pdf+html},
journal = {Proceedings of the Royal Society B: Biological Sciences}
}

@article{Stadler2011,
  title={Simulating trees with a fixed number of extant species},
  author={Stadler, Tanja},
  journal={Systematic biology},
  volume={60},
  number={5},
  pages={676--684},
  year={2011},
  publisher={Oxford University Press}
}

@Article{Rensch1948,
author = {Rensch, B.},
title = {Historical changes correlated with evolutionary changes of body size},
journal = {Evolution},
year = {1948},
OPTkey = {•},
volume = {2},
OPTnumber = {•},
pages = {218--230},
OPTmonth = {•},
OPTnote = {•},
OPTannote = {•}
}

@article{UyedaHarmon2014,
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repository: uyedaj/bmr

repo_name: uyedaj/bmr


text:
@article{gershman2015-computationalRationality,
  title={Computational rationality: A converging paradigm for intelligence in brains, minds, and machines},
  author={Gershman, Samuel J and Horvitz, Eric J and Tenenbaum, Joshua B},
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  pages={273--278},
  year={2015},
  publisher={American Association for the Advancement of Science}
}

@inbook{newell1981-skillAcquisitionAndLawOfPractice,
  chapter={Mechanisms of skill acquisition and the law of practice},
  title={Cognitive skills and their acquisition},
  author={Newell, Allen and Rosenbloom, Paul S and Anderson, John R},
  publisher={Psychology Press},
  pages={1--55},
  year={1981}
}

license_type: permissive

branch_name: refs/heads/master

extension: bib


text:
DESCRIPTION = "libdvbpsi is a simple library designed for decoding \
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HOMEPAGE = "http://www.videolan.org/developers/libdvbpsi.html"
LICENSE = "LGPL-2.1-only"
LIC_FILES_CHKSUM = "file://COPYING;md5=4fbd65380cdd255951079008b364516c"

SRC_URI = "http://download.videolan.org/pub/libdvbpsi/${PV}/libdvbpsi-${PV}.tar.bz2"
SRC_URI[md5sum] = "2b217039a1299000c39423441f77e76a"
SRC_URI[sha256sum] = "a2fed1d11980662f919bbd1f29e2462719e0f6227e1a531310bd5a706db0a1fe"

inherit autotools

license: MIT

repository: openembedded/meta-openembedded

repo_name: openembedded/meta-openembedded

gha_license_id: MIT

gha_language: BitBake

extension: bb


text:
@article{pmid36445439,
 author = {Niiranen, T. J. },
 journal = {Blood Press Monit},
 month = {Dec},
 number = {Suppl 1},
 pages = {e9-e10},
 title = {Translating GWAS data into cardiovascular disease prevention - the Finnish experience},
 volume = {27},
 year = {2022}
}

repository: hypertensioncenter/academic-kickstart

repo_name: hypertensioncenter/academic-kickstart

gha_language: TeX


text:
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# Commands may need to know the format version.
set(CMAKE_IMPORT_FILE_VERSION 1)

# Import target "Snappy::snappy" for configuration "Debug"
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list(APPEND _IMPORT_CHECK_TARGETS Snappy::snappy )
list(APPEND _IMPORT_CHECK_FILES_FOR_Snappy::snappy "${_IMPORT_PREFIX}/lib/libsnappy.so" )

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set(CMAKE_IMPORT_FILE_VERSION)

repository: lrzpellegrini/CL-CORe-App

repo_name: lrzpellegrini/CL-CORe-App

extension: cmake