text:
76,
  title={Natural selection and random genetic drift in phenotypic evolution},
  author={Lande, Russell},
  journal={Evolution},
  pages={314--334},
  year={1976},
  publisher={JSTOR}
}

@article{LandeArnold1983,
  title={The measurement of selection on correlated characters},
  author={Lande, Russell and Arnold, Stevan J},
  journal={Evolution},
  pages={1210--1226},
  year={1983},
  publisher={JSTOR}
}

@article{Arnold2001,
  title={The adaptive landscape as a conceptual bridge between micro-and macroevolution},
  author={Arnold, Stevan J and Pfrender, Michael E and Jones, Adam G},
  journal={Genetica},
  volume={112},
  number={1},
  pages={9--32},
  year={2001},
  publisher={Springer}
}

@article{Eastman2011,
	Author = {Eastman, Jonathan M. and Alfaro, Michael E. and Joyce, Paul and Hipp, Andrew L. and Harmon, Luke J.},
	Doi = {10.1111/j.1558-5646.2011.01401.x},
	Journal = {Evolution},
	Number = {12},
	Pages = {3578--3589},
	Title = {A Novel Comparative Method for Identifying Shifts in the Rate of Character Evolution on Trees},
	Volume = {65},
	Year = {2011},
	Bdsk-Url-1 = {http://dx.doi.org/10.1111/j.1558-5646.2011.01401.x}}

@article{FitzJohn2010,
author = {FitzJohn, Richard G.},
title = {Quantitative Traits and Diversification},
volume = {59},
number = {6},
pages = {619-633},
year = {2010},
doi = {10.1093/sysbio/syq053},
abstract ={Quantitative traits have long been hypothesized to affect speciation and extinction rates. For example, smaller body size or increased specialization may be associated with increased rates of diversification. Here, I present a phylogenetic likelihood-based method (quantitative state speciation and extinction [QuaSSE]) that can be used to test such hypotheses using extant character distributions. This approach assumes that diversification follows a birth‚Äìdeath process where speciation and extinction rates may vary with one or more traits that evolve under a diffusion model. Speciation and extinction rates may be arbitrary functions of the character state, allowing much flexibility in testing models of trait-dependent diversification. I test the approach using simulated phylogenies and show that a known relationship between speciation and a quantitative character could be recovered in up to 80% of the cases on large trees (500 species). Consistent with other approaches, detecting shifts in diversification due to differences in extinction rates was harder than when due to differences in speciation rates. Finally, I demonstrate the application of QuaSSE to investigate the correlation between body size and diversification in primates, concluding that clade-specific differences in diversification may be more important than size-dependent diversification in shaping the patterns of diversity within this group.},
URL = {http://sysbio.oxfordjournals.org/content/59/6/619.abstract},
eprint = {http://sysbio.oxfordjournals.org/content/59/6/619.full.pdf+html},
journal = {Systematic Biology}
}

@article {Fitzjohn2012,
author = {FitzJohn, Richard G.},
title = {Diversitree: comparative phylogenetic analyses of diversification in {R}},
journal = {Methods in Ecology and Evolution},
volume = {3},
number = {6},
publisher = {Blackwell Publishing Ltd},
issn = {2041-210X},
url = {http://dx.doi.org/10.1111/j.2041-210X.2012.00234.x},
doi = {10.1111/j.2041-210X.2012.00234.x},
pages = {1084--1092},
keywords = {birth–death process, comparative methods, extinction, macroevolution, speciation},
year = {2012},
}

@article{Uyeda2011,
author = {Uyeda, Josef C. and Hansen, Thomas F. and Arnold, Stevan J. and Pienaar, Jason},
title = {The million-year wait for macroevolutionary bursts},
volume = {108},
number = {38},
pages = {15908--15913},
year = {2011},
doi = {10.1073/pnas.1014503108},
abstract ={We lack a comprehensive understanding of evolutionary pattern and process because short-term and long-term data have rarely been combined into a single analytical framework. Here we test alternative models of phenotypic evolution using a dataset of unprecedented size and temporal span (over 8,000 data points). The data are body-size measurements taken from historical studies, the fossil record, and among-species comparative data representing mammals, squamates, and birds. By analyzing this large dataset, we identify stochastic models that can explain evolutionary patterns on both short and long timescales and reveal a remarkably consistent pattern in the timing of divergence across taxonomic groups. Even though rapid, short-term evolution often occurs in intervals shorter than 1 Myr, the changes are constrained and do not accumulate over time. Over longer intervals (1–360 Myr), this pattern of bounded evolution yields to a pattern of increasing divergence with time. The best-fitting model to explain this pattern is a model that combines rare but substantial bursts of phenotypic change with bounded fluctuations on shorter timescales. We suggest that these rare bursts reflect permanent changes in adaptive zones, whereas the short-term fluctuations represent local variations in niche optima due to restricted environmental variation within a stable adaptive zone.},
URL = {http://www.pnas.org/content/108/38/15908.abstract},
eprint = {http://www.pnas.org/content/108/38/15908.full.pdf+html},
journal = {Proceedings of the National Academy of Sciences}
}

@article{EstesArnold2007,
     jstor_articletype = {research-article},
     title = {Resolving the Paradox of Stasis: Models with Stabilizing Selection Explain Evolutionary Divergence on All Timescales.},
     author = {Suzanne Estes and Stevan J. Arnold},
     journal = {The American Naturalist},
     jstor_issuetitle = {},
     volume = {169},
     number = {2},
     jstor_formatteddate = {February 2007},
     pages = {227-244},
     url = {http://www.jstor.org/stable/10.1086/510633},
     ISSN = {00030147},
     abstract = {Abstract: We tested the ability of six quantitative genetic models to explain the evolution of phenotypic means using an extensive database compiled by Gingerich. Our approach differs from past efforts in that we use explicit models of evolutionary process, with parameters estimated from contemporary populations, to analyze a large sample of divergence data on many different timescales. We show that one quantitative genetic model yields a good fit to data on phenotypic divergence across timescales ranging from a few generations to 10 million generations. The key feature of this model is a fitness optimum that moves within fixed limits. Conversely, a model of neutral evolution, models with a stationary optimum that undergoes Brownian or white noise motion, a model with a moving optimum, and a peak shift model all fail to account for the data on most or all timescales. We discuss our results within the framework of Simpson’s concept of adaptive landscapes and zones. Our analysis suggests that the underlying process causing phenotypic stasis is adaptation to an optimum that moves within an adaptive zone with stable boundaries. We discuss the implication of our results for comparative studies and phylogeny inference based on phenotypic characters.},
     year = {2007},
     publisher = {The University of Chicago Press for The American Society of Naturalists},
     copyright = {Copyright © 2007 The University of Chicago},
    }

@article{Hunt2012,
author = {Hunt, Gene},
title = {Measuring rates of phenotypic evolution and the inseparability of tempo and mode},
volume = {38},
number = {3},
pages = {351-373},
year = {2012},
doi = {10.1666/11047.1},
abstract ={Rates of phenotypic evolution are central to many issues in paleontology, but traditional rate metrics such as darwins or haldanes are seldom used because of their strong dependence on interval length. In this paper, I argue that rates are usefully thought of as model parameters that relate magnitudes of evolutionary divergence to elapsed time. Starting with models of directional evolution, random walks, and stasis, I derive for each a reasonable rate metric. These metrics can be linked to existing approaches in evolutionary biology, and simulations show that they can be estimated accurately at any temporal resolution via maximum likelihood, but only when that metric's underlying model is true.The estimation of generational rates of a random walk under realistic paleontological conditions is compared with simulations to that of a prominent alternative approach, Gingerich's LRI (log-rate, log-interval) method. Generational rates are estimated poorly by LRI; they often reflect sampling error more than the actual pace of change. Further simulations show that under some realistic conditions, it is simply not possible to infer generational rates from coarsely sampled populations.These modeling results indicate a complex dependence between evolutionary mode and the measurement of evolutionary rates, and that there is unlikely to be a rate metric that works well for all traits and time scales. Compilations of paleontological and phylogenetic data indicate that all of the three rate metrics derived here show some relationship with interval length. Although there is no perfect rate metric, at present the most practical choices derive from the parameters of the stasis and random walk models. The latter, called the step variance, is particularly promising as a rate metric in paleontology and comparative biology.},
URL = {http://paleobiol.geoscienceworld.org/content/38/3/351.abstract},
eprint = {http://paleobiol.geoscienceworld.org/content/38/3/351.full.pdf+html},
journal = {Paleobiology}
}

@article{Strotz2013,
author = {Strotz, Luke C. and Allen, Andrew P.},
title = {Assessing the role of cladogenesis in macroevolution by integrating fossil and molecular evidence},
volume = {110},
number = {8},
pages = {2904--2909},
year = {2013},
doi = {10.1073/pnas.1208302110},
abstract ={Assessing the extent to which population subdivision during cladogenesis is necessary for long-term phenotypic evolution is of fundamental importance in a broad range of biological disciplines. Differentiating cladogenesis from anagenesis, defined as evolution within a species, has generally been hampered by dating precision, insufficient fossil data, and difficulties in establishing a direct link between morphological changes detectable in the fossil record and biological species. Here we quantify the relative frequencies of cladogenesis and anagenesis for macroperforate planktic Foraminifera, which arguably have the most complete fossil record currently available, to address this question. Analyzing this record in light of molecular evidence, while taking into account the precision of fossil dating techniques, we estimate that the fraction of speciation events attributable to anagenesis is <19% during the Cenozoic era (last 65 Myr) and <10% during the Neogene period (last 23 Myr). Our central conclusion—that cladogenesis is the predominant mode by which new planktic Foraminifera taxa become established at macroevolutionary time scales—differs markedly from the conclusion reached in a recent study based solely on fossil data. These disparate findings demonstrate that interpretations of macroevolutionary dynamics in the fossil record can be fundamentally altered in light of genetic evidence.},
URL = {http://www.pnas.org/content/110/8/2904.abstract},
eprint = {http://www.pnas.org/content/110/8/2904.full.pdf+html},
journal = {Proceedings of the National Academy of Sciences}
}

@article{Hunt2007,
	Abstract = {The nature of evolutionary changes recorded by the fossil record has long been controversial, with particular disagreement concerning the relative frequency of gradual change versus stasis within lineages. Here, I present a large-scale, statistical survey of evolutionary mode in fossil lineages. Over 250 sequences of evolving traits were fit by using maximum likelihood to three evolutionary models: directional change, random walk, and stasis. Evolution in these traits was rarely directional; in only 5% of fossil sequences was directional evolution the most strongly supported of the three modes of change. The remaining 95% of sequences were divided nearly equally between random walks and stasis. Variables related to body size were significantly less likely than shape traits to experience stasis. This finding is in accord with previous suggestions that size may be more evolutionarily labile than shape and is consistent with some but not all of the mechanisms proposed to explain evolutionary stasis. In general, similar evolutionary patterns are observed across other variables, such as clade membership and temporal resolution, but there is some evidence that directional change in planktonic organisms is more frequent than in benthic organisms. The rarity with which directional evolution was observed in this study corroborates a key claim of punctuated equilibria and suggests that truly directional evolution is infrequent or, perhaps more importantly, of short enough duration so as to rarely register in paleontological sampling.},
	Author = {Hunt, Gene},
	Date-Added = {2012-11-14 17:50:13 -0500},
	Date-Modified = {2012-11-14 17:50:21 -0500},
	Doi = {10.1073/pnas.0704088104},
	Eprint = {http://www.pnas.org/content/104/47/18404.full.pdf+html},
	Journal = {Proceedings of the National Academy of Sciences},
	Number = {47},
	Pages = {18404-18408},
	Title = {The relative importance of directional change, random walks, and stasis in the evolution of fossil lineages},
	Url = {http://www.pnas.org/content/104/47/18404.abstract},
	Volume = {104},
	Year = {2007},
	Bdsk-Url-1 = {http://www.pnas.org/content/104/47/18404.abstract},
	Bdsk-Url-2 = {http://dx.doi.org/10.1073/pnas.0704088104}}

@article{Ingram2011,
author = {Ingram, Travis},
title = {Speciation along a depth gradient in a marine adaptive radiation},
volume = {278},
number = {1705},
pages = {613-618},
year = {2011},
doi = {10.1098/rspb.2010.1127},
abstract ={Oceans are home to much of the world's biodiversity, but we know little about the processes driving speciation in marine ecosystems with few geographical barriers to gene flow. Ecological speciation resulting from divergent natural selection between ecological niches can occur in the face of gene flow. Sister species in the young and ecologically diverse rockfish genus Sebastes coexist in the northeast Pacific, implying that speciation may not require geographical isolation. Here, I use a novel phylogenetic comparative analysis to show that rockfish speciation is instead associated with divergence in habitat depth and depth-associated morphology, consistent with models of parapatric speciation. Using the same analysis, I find no support for alternative hypotheses that speciation involves divergence in diet or life history, or that speciation involves geographic isolation by latitude. These findings support the hypothesis that rockfishes undergo ecological speciation on an environmental gradient.},
URL = {http://rspb.royalsocietypublishing.org/content/278/1705/613.abstract},
eprint = {http://rspb.royalsocietypublishing.org/content/278/1705/613.full.pdf+html},
journal = {Proceedings of the Royal Society B: Biological Sciences}
}

@article{Grey2008,
author = {Grey, Melissa and Haggart, James W. and Smith, Paul L.},
title = {Variation in Evolutionary Patterns Across the Geographic Range of a Fossil Bivalve},
volume = {322},
number = {5905},
pages = {1238-1241},
year = {2008},
doi = {10.1126/science.1162046},
abstract ={The fossil record is the only direct source of data for studying modes (patterns) and rates of morphological change over long periods of time. Determining modes and rates is important for understanding macroevolutionary processes, but just how modes and rates vary within a taxon, and why, remain largely unaddressed. We examined patterns of morphological change in the shell of the Mesozoic marine bivalve genus Buchia over its geographic and temporal range. Most modes conformed to either random walks or stasis, and both modes and rates showed variability between locations. For example, stasis was more common in deeper marine environments, whereas random walks occurred more often at the highest paleolatitudes studied. These results indicate that the environment can play an important role in shaping patterns of evolution.},
URL = {http://www.sciencemag.org/content/322/5905/1238.abstract},
eprint = {http://www.sciencemag.org/content/322/5905/1238.full.pdf},
journal = {Science}
}

@article {Bokma2008,
author = {Bokma, Folmer},
title = {Detection of ``Punctuated Equilibrium'' by {B}ayesian Estimation of Speciation and Extinction Rates, Ancestral Character States, and Rates of Anagenetic and Cladogenetic Evolution on a Molecular Phylogeny},
journal = {Evolution},
volume = {62},
number = {11},
publisher = {Blackwell Publishing Inc},
issn = {1558-5646},
url = {http://dx.doi.org/10.1111/j.1558-5646.2008.00492.x},
doi = {10.1111/j.1558-5646.2008.00492.x},
pages = {2718--2726},
keywords = {Cladogenesis, gene expression, macroevolution, molecular phylogenetics, stasis},
year = {2008},
}

@article {Bokma2002,
author = {Bokma, F.},
title = {Detection of punctuated equilibrium from molecular phylogenies},
journal = {Journal of Evolutionary Biology},
volume = {15},
number = {6},
publisher = {Blackwell Science Ltd},
issn = {1420-9101},
url = {http://dx.doi.org/10.1046/j.1420-9101.2002.00458.x},
doi = {10.1046/j.1420-9101.2002.00458.x},
pages = {1048--1056},
keywords = {macroevolution, maximum likelihood, phyletic gradualism, punctuated equilibrium, speciation},
year = {2002},
}

@article{Pagel2006,
author = {Pagel, Mark and Venditti, Chris and Meade, Andrew},
title = {Large Punctuational Contribution of Speciation to Evolutionary Divergence at the Molecular Level},
volume = {314},
number = {5796},
pages = {119-121},
year = {2006},
doi = {10.1126/science.1129647},
abstract ={A long-standing debate in evolutionary biology concerns whether species diverge gradually through time or by punctuational episodes at the time of speciation. We found that approximately 22% of substitutional changes at the DNA level can be attributed to punctuational evolution, and the remainder accumulates from background gradual divergence. Punctuational effects occur at more than twice the rate in plants and fungi than in animals, but the proportion of total divergence attributable to punctuational change does not vary among these groups. Punctuational changes cause departures from a clock-like tempo of evolution, suggesting that they should be accounted for in deriving dates from phylogenies. Punctuational episodes of evolution may play a larger role in promoting evolutionary divergence than has previously been appreciated.},
URL = {http://www.sciencemag.org/content/314/5796/119.abstract},
eprint = {http://www.sciencemag.org/content/314/5796/119.full.pdf},
journal = {Science}
}

@article{Atkinson2008,
author = {Atkinson, Quentin D. and Meade, Andrew and Venditti, Chris and Greenhill, Simon J. and Pagel, Mark},
title = {Languages Evolve in Punctuational Bursts},
volume = {319},
number = {5863},
pages = {588},
year = {2008},
doi = {10.1126/science.1149683},
abstract ={Linguists speculate that human languages often evolve in rapid or punctuational bursts, sometimes associated with their emergence from other languages, but this phenomenon has never been demonstrated. We used vocabulary data from three of the world's major language groups---Bantu, Indo-European, and Austronesian---to show that 10 to 33% of the overall vocabulary differences among these languages arose from rapid bursts of change associated with language-splitting events. Our findings identify a general tendency for increased rates of linguistic evolution in fledgling languages, perhaps arising from a linguistic founder effect or a desire to establish a distinct social identity.},
URL = {http://www.sciencemag.org/content/319/5863/588.abstract},
eprint = {http://www.sciencemag.org/content/319/5863/588.full.pdf},
journal = {Science}
}

@Article{Hopkins2012,
author = {Hopkins, Melanie J. and Lidgard, Scott},
title = {Evolutionary mode routinely varies among morphological traits within fossil species lineages},
journal = {Proceedings of the National Academy of Sciences},
year = {2012},
OPTkey = {•},
volume = {109},
OPTnumber = {•},
pages = {20520--20525},
OPTmonth = {•},
OPTnote = {•},
OPTannote = {•}
}

@article {Simpson2013,
author = {Simpson, Carl},
title = {Species selection and the macroevolution of coral coloniality and photosymbiosis},
journal = {Evolution},
volume = {67},
number = {6},
issn = {1558-5646},
url = {http://dx.doi.org/10.1111/evo.12083},
doi = {10.1111/evo.12083},
pages = {1607--1621},
keywords = {Diversification, multilevel selection, multivariate selection, paleobiology, phylogenetics},
year = {2013},
}

@article {Rabosky2012,
author = {Rabosky, Daniel L.},
title = {Positive correlation between diversification rates and phenotypic evolvability can mimic punctuated equilibrium on molecular phylogenies},
journal = {Evolution},
volume = {66},
number = {8},
publisher = {Blackwell Publishing Inc},
issn = {1558-5646},
url = {http://dx.doi.org/10.1111/j.1558-5646.2012.01631.x},
doi = {10.1111/j.1558-5646.2012.01631.x},
pages = {2622--2627},
keywords = {Adaptive radiation, macroevolution, morphological evolution, speciation},
year = {2012},
}

@article {Huntetal2008,
author = {Hunt, Gene and Bell, Michael A. and Travis, Matthew P.},
title = {Evolution toward a new adaptive optimum: phenotypic evolution in a fossil stickleback lineage},
journal = {Evolution},
volume = {62},
number = {3},
publisher = {Blackwell Publishing Inc},
issn = {1558-5646},
url = {http://dx.doi.org/10.1111/j.1558-5646.2007.00310.x},
doi = {10.1111/j.1558-5646.2007.00310.x},
pages = {700--710},
keywords = {Adaptive evolution, adaptive landscape, neutral evolution, random walk, stickleback, time series, Orstein–Uhlenbeck process},
year = {2008},
}

@article{Landis2012,
author = {Landis, Michael J. and Schraiber, Joshua G. and Liang, Mason},
title = {Phylogenetic Analysis Using {L}\'{e}vy Processes: Finding Jumps in the Evolution of Continuous Traits},
volume = {62},
number = {2},
pages = {193--204},
year = {2013},
doi = {10.1093/sysbio/sys086},
abstract ={Gaussian processes, a class of stochastic processes including Brownian motion and the Ornstein–Uhlenbeck process, are widely used to model continuous trait evolution in statistical phylogenetics. Under such processes, observations at the tips of a phylogenetic tree have a multivariate Gaussian distribution, which may lead to suboptimal model specification under certain evolutionary conditions, as supposed in models of punctuated equilibrium or adaptive radiation. To consider non-normally distributed continuous trait evolution, we introduce a method to compute posterior probabilities when modeling continuous trait evolution as a Lévy process. Through data simulation and model testing, we establish that single-rate Brownian motion (BM) and Lévy processes with jumps generate distinct patterns in comparative data. We then analyzed body mass and endocranial volume measurements for 126 primates. We rejected single-rate BM in favor of a Lévy process with jumps for each trait, with the lineage leading to most recent common ancestor of great apes showing particularly strong evidence against single-rate BM. [Continuous traits; saltational evolution; Lévy processes; Bayesian inference.]},
URL = {http://sysbio.oxfordjournals.org/content/62/2/193.abstract},
eprint = {http://sysbio.oxfordjournals.org/content/62/2/193.full.pdf+html},
journal = {Systematic Biology}
}

@Misc{Bartoszek2013,
OPTkey = {•},
author = {Bartoszek, Krzysztof},
title = {Quantifying the effects of anagenetic and cladogenetic evolution},
OPThowpublished = {•},
OPTmonth = {•},
year = {2013},
note = {arXiv:1305.2378},
OPTannote = {•}
}

@Article{Rabosky2013,
author = {Rabosky, Daniel L. and Santini, Francesco and Eastman, Jonathan and Smith, Stephen A. and Sidlauskus, Brian and Chang, Jonathan and Alfaro, Michael E.},
title = {Rates of speciation and morphological evolution are correlated across the largest vertebrate radiation},
journal = {Nature Communications},
year = {2013},
OPTkey = {•},
volume = {4},
OPTnumber = {•},
OPTpages = {•},
OPTmonth = {•},
OPTnote = {•},
OPTannote = {•}
}

@article{Baca2013,
title = "Punctuated Evolution of Prostate Cancer Genomes ",
journal = "Cell ",
volume = "153",
number = "3",
pages = "666--677",
year = "2013",
note = "",
issn = "0092-8674",
doi = "10.1016/j.cell.2013.03.021",
url = "http://www.sciencedirect.com/science/article/pii/S0092867413003437",
author = "Sylvan C. Baca and Davide Prandi and Michael S. Lawrence and Juan Miguel Mosquera and Alessandro Romanel and Yotam Drier and Kyung Park and Naoki Kitabayashi and Theresa Y. MacDonald and Mahmoud Ghandi and Eliezer Van Allen and Gregory V. Kryukov and Andrea Sboner and Jean-Philippe Theurillat and T. David Soong and Elizabeth Nickerson and Daniel Auclair and Ashutosh Tewari and Himisha Beltran and Robert C. Onofrio and Gunther Boysen and Candace Guiducci and Christopher E. Barbieri and Kristian Cibulskis and Andrey Sivachenko and Scott L. Carter and Gordon Saksena and Douglas Voet and Alex H. Ramos and Wendy Winckler and Michelle Cipicchio and Kristin Ardlie and Philip W. Kantoff and Michael F. Berger and Stacey B. Gabriel and Todd R. Golub and Matthew Meyerson and Eric S. Lander and Olivier Elemento and Gad Getz and Francesca Demichelis and Mark A. Rubin and Levi A. Garraway"
}

@article{GouldEldredge1977,
     jstor_articletype = {research-article},
     title = {Punctuated Equilibria: The Tempo and Mode of Evolution Reconsidered},
     author = {Gould, Stephen Jay and Eldredge, Niles},
     journal = {Paleobiology},
     jstor_issuetitle = {},
     volume = {3},
     number = {2},
     jstor_formatteddate = {Spring, 1977},
     pages = {115--151},
     url = {http://www.jstor.org/stable/2400177},
     ISSN = {00948373},
     abstract = {We believe that punctuational change dominates the history of life: evolution is concentrated in very rapid events of speciation (geologically instantaneous, even if tolerably continuous in ecological time). Most species, during their geological history, either do not change in any appreciable way, or else they fluctuate mildly in morphology, with no apparent direction. Phyletic gradualism is very rare and too slow, in any case, to produce the major events of evolution. Evolutionary trends are not the product of slow, directional transformation within lineages; they represent the differential success of certain species within a clade-speciation may be random with respect to the direction of a trend (Wright's rule). As an a priori bias, phyletic gradualism has precluded any fair assessment of evolutionary tempos and modes. It could not be refuted by empirical catalogues constructed in its light because it excluded contrary information as the artificial result of an imperfect fossil record. With the model of punctuated equilibria, an unbiased distribution of evolutionary tempos can be established by treating stasis as data and by recording the pattern of change for all species in an assemblage. This distribution of tempos can lead to strong inferences about modes. If, as we predict, the punctuational tempo is prevalent, then speciation-not phyletic evolution-must be the dominant mode of evolution. We argue that virtually none of the examples brought forward to refute our model can stand as support for phyletic gradualism; many are so weak and ambiguous that they only reflect the persistent bias for gradualism still deeply embedded in paleontological thought. Of the few stronger cases, we concentrate on Gingerich's data for Hyopsodus and argue that it provides an excellent example of species selection under our model. We then review the data of several studies that have supported our model since we published it five years ago. The record of human evolution seems to provide a particularly good example: no gradualism has been detected within any hominid taxon, and many are long-ranging; the trend to larger brains arises from differential success of essentially static taxa. The data of molecular genetics support our assumption that large genetic changes often accompany the process of speciation. Phyletic gradualism was an a priori assertion from the start-it was never "seen" in the rocks; it expressed the cultural and political biases of 19th century liberalism. Huxley advised Darwin to eschew it as an "unnecessary difficulty." We think that it has now become an empirical fallacy. A punctuational view of change may have wide validity at all levels of evolutionary processes. At the very least, it deserves consideration as an alternate way of interpreting the history of life.},
     language = {English},
     year = {1977},
     publisher = {Paleontological Society},
     copyright = {Copyright © 1977 Paleontological Society},
    }

@article{Eldredge1971,
     jstor_articletype = {research-article},
     title = {The Allopatric Model and Phylogeny in Paleozoic Invertebrates},
     author = {Eldredge, Niles},
     journal = {Evolution},
     jstor_issuetitle = {},
     volume = {25},
     number = {1},
     jstor_formatteddate = {Mar., 1971},
     pages = {156--167},
     url = {http://www.jstor.org/stable/2406508},
     ISSN = {00143820},
     abstract = {Emphasis on time and gradualistic transformation has led to the dominance of a strictly phyletic model of species transformation in most paleontological thought. Even documented cases of lineage-splitting are often interpreted by recourse to a gradual (morphological) divergence model in which a strong element of phyletic thinking is incorporated. Allopatric speciation, not a strict alternative to gradual divergence, seems to fit the common pattern of non-intergrading species within a lineage as typically preserved in Paleozoic epeiric sediments. The majority of species preserved in epeiric sediments show no change in species-specific characters throughout the interval of their stratigraphic occurrence, and the phyletic model is inapplicable to most of these elements of the fossil record. Instead, change in, or development of, species-specific characters are envisioned as occurring relatively rapidly in peripheral isolates. Morphological stability of epeiric species is attributed to stabilizing selection. The Devonian trilobite Phacops rana illustrates, at two different times in its history, the origin of a new character state in peripheral isolates. Most new Paleozoic invertebrate taxa probably arose in geosynclines (marginal seas) bordering the cratons; though these origination events themselves were probably not related to marine regressions, invasion of new taxa into the epeiric seas seems directly related to periods of transgression.},
     language = {English},
     year = {1971},
     publisher = {Society for the Study of Evolution},
     copyright = {Copyright © 1971 Society for the Study of Evolution},
    }

@InCollection{EldredgeGould1972,
author = {Eldredge, Niles and Gould, Stephen Jay},
title = {Punctuated equilibria: an alternative to phyletic gradualism},
booktitle = {Models in Paleobiology},
OPTcrossref = {•},
OPTkey = {•},
pages = {82--115},
publisher = {Freman, Cooper \& Co.},
year = {1972},
editor = {TJM Schopf},
OPTvolume = {•},
OPTnumber = {•},
OPTseries = {•},
OPTtype = {•},
OPTchapter = {•},
OPTaddress = {•},
OPTedition = {•},
OPTmonth = {•},
OPTnote = {•},
OPTannote = {•}
}

@article{Stanley1975,
author = {Stanley, S M},
title = {A theory of evolution above the species level},
volume = {72},
number = {2},
pages = {646--650},
year = {1975},
abstract ={Gradual evolutionary change by natural selection operates so slowly within established species that it cannot account for the major features of evolution. Evolutionary change tends to be concentrated within speciation events. The direction of transpecific evolution is determined by the process of species selection, which is analogous to natural selection but acts upon species within higher taxa rather than upon individuals within populations. Species selection operates on variation provided by the largely random process of speciation and favors species that speciate at high rates or survive for long periods and therefore tend to leave many daughter species. Rates of speciation can be estimated for living taxa by means of the equation for exponential increase, and are clearly higher for mammals than for bivalve mollusks.},
URL = {http://www.pnas.org/content/72/2/646.abstract},
eprint = {http://www.pnas.org/content/72/2/646.full.pdf+html},
journal = {Proceedings of the National Academy of Sciences}
}

@Book{Stanley1979,
author = {Stanley, Steven},
ALTeditor = {•},
title = {Macroevolution},
publisher = {Johns Hopkins University Press},
year = {1979},
OPTkey = {•},
OPTvolume = {•},
OPTnumber = {•},
OPTseries = {•},
OPTaddress = {•},
OPTedition = {•},
OPTmonth = {•},
OPTnote = {•},
OPTannote = {•}
}

@article{Charlesworth1982,
     jstor_articletype = {research-article},
     title = {A Neo-{D}arwinian Commentary on Macroevolution},
     author = {Charlesworth, Brian and Lande, Russell and Slatkin, Montgomery},
     journal = {Evolution},
     jstor_issuetitle = {},
     volume = {36},
     number = {3},
     jstor_formatteddate = {May, 1982},
     pages = {474--498},
     url = {http://www.jstor.org/stable/2408095},
     ISSN = {00143820},
     abstract = {},
     language = {English},
     year = {1982},
     publisher = {Society for the Study of Evolution},
     copyright = {Copyright © 1982 Society for the Study of Evolution},
    }

@article{Omeara2006,
	Author = {O'Meara, Brian C. and An{\'e}, C{\'e}cile and Sanderson, Michael J. and Wainwright, Peter C.},
	Doi = {10.1111/j.0014-3820.2006.tb01171.x},
	Issn = {1558-5646},
	Journal = {Evolution},
	Number = {5},
	Pages = {922--933},
	Title = {Testing for Different Rates of Continuous Trait Evolution Using Likelihood},
	Volume = {60},
	Year = {2006},
	Bdsk-Url-1 = {http://dx.doi.org/10.1111/j.0014-3820.2006.tb01171.x}}}

@Misc{Eastmanjump,
OPTkey = {•},
author = {Eastman, Jonathan M. and Wegmann, Daniel and Leuenberger, Christoph and Harmon, Luke J.},
title = {Simpsonian `Evolution by Jumps' in an Adaptive Radiation of \textit{Anolis} Lizards},
OPThowpublished = {•},
OPTmonth = {•},
year = {2013},
note = {arXiv:1305.4216},
OPTannote = {•}
}

@article{Pennell2014geiger,
  title={geiger v2. 0: an expanded suite of methods for fitting macroevolutionary models to phylogenetic trees},
  author={Pennell, Matthew W and Eastman, Jonathan M and Slater, Graham J and Brown, Joseph W and Uyeda, Josef C and FitzJohn, Richard G and Alfaro, Michael E and Harmon, Luke J},
  journal={Bioinformatics},
  pages={btu181},
  year={2014},
  publisher={Oxford Univ Press}
}

@article {PennellHarmon,
author = {Pennell, Matthew W. and Harmon, Luke J.},
title = {An integrative view of phylogenetic comparative methods: connections to population genetics, community ecology, and paleobiology},
journal = {Annals of the New York Academy of Sciences},
volume = {1289},
number = {1},
issn = {1749-6632},
url = {http://dx.doi.org/10.1111/nyas.12157},
doi = {10.1111/nyas.12157},
pages = {90--105},
keywords = {macroevolution, phylogenies, fossils},
year = {2013},
}

@article{Omeara2012,
author = {O'Meara, Brian C.},
title = {Evolutionary Inferences from Phylogenies: A Review of Methods},
journal = {Annual Review of Ecology, Evolution, and Systematics},
volume = {43},
number = {1},
pages = {267--285},
year = {2012},
doi = {10.1146/annurev-ecolsys-110411-160331},

URL = {http://www.annualreviews.org/doi/abs/10.1146/annurev-ecolsys-110411-160331},
eprint = {http://www.annualreviews.org/doi/pdf/10.1146/annurev-ecolsys-110411-160331}
}

@article{Slater2012MECCA,
	Author = {Slater, Graham J. and Harmon, Luke J. and Wegmann, Daniel and Joyce, Paul and Revell, Liam J. and Alfaro, Michael E.},
	Doi = {10.1111/j.1558-5646.2011.01474.x},
	Journal = {Evolution},
	Number = {3},
	Pages = {752--762},
	Title = {Fitting Models of Continous Trait Evolution to Incompletely Sampled Comparative Data Using Approximate {B}ayesian Computation},
	Volume = {66},
	Year = {2012},
	Bdsk-Url-1 = {http://dx.doi.org/10.1111/j.1558-5646.2011.01474.x}}

@article {Slater2012Fossil,
author = {Slater, Graham J. and Harmon, Luke J. and Alfaro, Michael E.},
title = {Integrating Fossils with Molecular Phylogenies Improves Inference of Trait Evolution},
journal = {Evolution},
volume = {66},
number = {12},
publisher = {Blackwell Publishing Inc},
issn = {1558-5646},
url = {http://dx.doi.org/10.1111/j.1558-5646.2012.01723.x},
doi = {10.1111/j.1558-5646.2012.01723.x},
pages = {3931--3944},
keywords = {Ancestral states, Brownian motion, Caniformia, model selection, phylogenetic comparative methods},
year = {2012},
}
}

@Book{CoyneOrr,
author = {Coyne, Jerry A and Orr, H. Allen},
ALTeditor = {•},
title = {Speciation},
publisher = {Sinauer Associates},
year = {2004},
OPTkey = {•},
OPTvolume = {•},
OPTnumber = {•},
OPTseries = {•},
OPTaddress = {•},
OPTedition = {•},
OPTmonth = {•},
OPTnote = {•},
OPTannote = {•}
}

@article{RaboskyMcCune2010,
title = "Reinventing species selection with molecular phylogenies",
journal = "Trends in Ecology \& Evolution",
volume = "25",
number = "2",
pages = "68--74",
year = "2010",
note = "",
issn = "0169-5347",
doi = "10.1016/j.tree.2009.07.002",
url = "http://www.sciencedirect.com/science/article/pii/S0169534709002328",
author = "Daniel L. Rabosky and Amy R. McCune"
}

@article{Jablonski2008,
author = {Jablonski, David},
title = {Species Selection: Theory and Data},
journal = {Annual Review of Ecology, Evolution, and Systematics},
volume = {39},
number = {1},
pages = {501--524},
year = {2008},
doi = {10.1146/annurev.ecolsys.39.110707.173510},

URL = {http://www.annualreviews.org/doi/abs/10.1146/annurev.ecolsys.39.110707.173510},
eprint = {http://www.annualreviews.org/doi/pdf/10.1146/annurev.ecolsys.39.110707.173510}
}

@PhdThesis{FitzJohnthesis,
author = {Fitzjohn, Richard G.},
title = {What Drives Biological Diversification? Detecting Traits Under Species Selection},
school = {University of British Columbia},
year = {2012},
OPTkey = {•},
OPTtype = {•},
OPTaddress = {•},
OPTmonth = {•},
OPTnote = {•},
OPTannote = {•}
}

@article{Gould1980,
     jstor_articletype = {research-article},
     title = {Is a New and General Theory of Evolution Emerging?},
     author = {Gould, Stephen Jay},
     journal = {Paleobiology},
     jstor_issuetitle = {},
     volume = {6},
     number = {1},
     jstor_formatteddate = {Winter, 1980},
     pages = {119--130},
     url = {http://www.jstor.org/stable/2400240},
     ISSN = {00948373},
     abstract = {The modern synthesis, as an exclusive proposition, has broken down on both of its fundamental claims: extrapolationism (gradual allelic substitution as a model for all evolutionary change) and nearly exclusive reliance on selection leading to adaptation. Evolution is a hierarchical process with complementary, but different, modes of change at its three major levels: variation within populations, speciation, and patterns of macroevolution. Speciation is not always an extension of gradual, adaptive allelic substitution to greater effect, but may represent, as Goldschmidt argued, a different style of genetic change-rapid reorganization of the genome, perhaps non-adaptive. Macroevolutionary trends do not arise from the gradual, adaptive transformation of populations, but usually from a higher-order selection operating upon groups of species, while the individual species themselves generally do not change following their geologically instantaneous origin. I refer to these two discontinuities in the evolutionary hierarchy as the Goldschmidt break (between change in populations and speciation) and the Wright break (between speciation and trends as differential success among species). A new and general evolutionary theory will embody this notion of hierarchy and stress a variety of themes either ignored or explicitly rejected by the modern synthesis: punctuational change at all levels, important non-adaptive change at all levels, control of evolution not only by selection, but equally by constraints of history, development and architecture-thus restoring to evolutionary theory a concept of organism.},
     language = {English},
     year = {1980},
     publisher = {Paleontological Society},
     copyright = {Copyright © 1980 Paleontological Society},
    }

@article{Hannisdal2007,
     jstor_articletype = {research-article},
     title = {Inferring Phenotypic Evolution in the Fossil Record by {B}ayesian Inversion},
     author = {Hannisdal, Bjarte},
     journal = {Paleobiology},
     jstor_issuetitle = {},
     volume = {33},
     number = {1},
     jstor_formatteddate = {Winter, 2007},
     pages = {98--115},
     url = {http://www.jstor.org/stable/4500140},
     ISSN = {00948373},
     abstract = {This paper takes an alternative approach to the problem of inferring patterns of phenotypic evolution in the fossil record. Reconstructing temporal biological signal from noisy stratophenetic data is an inverse problem analogous to subsurface reconstructions in geophysics, and similar methods apply. To increase the information content of stratophenetic series, available geological data on sample ages and environments are included as prior knowledge, and all inferences are conditioned on the uncertainty in these geological variables. This uncertainty, as well as data error and the stochasticity of fossil preservation and evolution, prevents any unique solution to the stratophenetic inverse problem. Instead, the solution is defined as a distribution of model parameter values that explain the data to varying degrees. This distribution is obtained by direct Monte Carlo sampling of the parameter space, and evaluated with Bayesian integrals. The Bayesian inversion is illustrated with Miocene stratigraphic data from the ODP Leg 174AX Bethany Beach bore-hole. A sample of the benthic foraminifer Pseudononion pizarrensis is used to obtain a phenotypic covariance matrix for outline shape, which constrains a model of multivariate shape evolution. The forward model combines this evolutionary model and stochastic models of fossil occurrence with the empirical sedimentary record to generate predicted stratophenetic series. A synthetic data set is inverted, using the Neighbourhood Algorithm to sample the parameter space and characterize the posterior probability distribution. Despite small sample sizes and noisy shape data, most of the generating parameter values are well resolved, and the underlying pattern of phenotypic evolution can be reconstructed, with quantitative measures of uncertainty. Inversion of a stratigraphic series into a time series can significantly improve our perception and interpretation of an evolutionary pattern.},
     language = {English},
     year = {2007},
     publisher = {Paleontological Society},
     copyright = {Copyright © 2007 Paleontological Society},
    }

@Book{StratPaleobook,
author = {Patzkowsky, Mark E. and Holland, Steven M.},
ALTeditor = {•},
title = {Stratigraphic Paleobiology: Understanding the distribution of fossil taxa in time and space},
publisher = {University of Chicago Press},
year = {2012},
OPTkey = {•},
OPTvolume = {•},
OPTnumber = {•},
OPTseries = {•},
OPTaddress = {•},
OPTedition = {•},
OPTmonth = {•},
OPTnote = {•},
OPTannote = {•}
}

@article {Beaulieu2012,
author = {Beaulieu, Jeremy M. and Jhwueng, Dwueng-Chwuan and Boettiger, Carl and O'Meara, Brian C.},
title = {Modeling Stabilizing Selection: Expanding the {O}rnstein-{U}hlenbeck Model of Adaptive Evolution},
journal = {Evolution},
volume = {66},
number = {8},
publisher = {Blackwell Publishing Inc},
issn = {1558--5646},
url = {http://dx.doi.org/10.1111/j.1558-5646.2012.01619.x},
doi = {10.1111/j.1558-5646.2012.01619.x},
pages = {2369--2383},
keywords = {Brownian motion, comparative method, continuous characters Hansen model, Ornstein–Uhlenbeck},
year = {2012},
}

@article{HansenMartins1996,
	Abstract = {As species evolve along a phylogenetic tree, we expect closely related species to retain some phenotypic similarities due to their shared evolutionary histories. The amount of expected similarity depends both on the hierarchical phylogenetic structure, and on the specific magnitude and types of evolutionary changes that accumulate during each generation. In this study, we show how models of microevolutionary change can be translated into the resulting macroevolutionary patterns. We illustrate how the structure of phenotypic covariances expected in interspecific measurements can be derived, and how this structure depends on the microevolutionary forces guiding phenotypic change at each generation. We then explore the covariance structure expected from several simple macroevolutionary models of phenotypic evolution, including various combinations of random genetic drift, directional selection, stabilizing selection, and environmental change, as well as models of punctuated or burst-like evolution. We find that stabilizing selection leads to patterns of exponential decrease of between species covariance with phylogenetic distance. This is different from the usual linear patterns of decrease assumed in most comparative and systematic methods. Nevertheless, linear patterns of decrease can result from many processes in addition to random genetic drift, such as directional and fluctuating selection as well as modes of punctuated change. Our framework can be used to develop methods for (1) phylogenetic reconstruction; (2) inference of the evolutionary process from comparative data; and (3) conducting or evaluating statistical analyses of comparative data while taking phylogenetic history into account.},
	Author = {Hansen, Thomas F. and Martins, Emilia P.},
	Journal = {Evolution},
	Number = {4},
	Pages = {1404--1417},
	Title = {Translating Between Microevolutionary Process and Macroevolutionary Patterns: The Correlation Structure of Interspecific Data},
	Volume = {50},
	Year = {1996}}

@article{Khaitovich2005,
author = {Khaitovich, Philipp and P\"{a}\"{a}bo, Svante and Weiss, Gunter},
title = {Toward a Neutral Evolutionary Model of Gene Expression},
volume = {170},
number = {2},
pages = {929--939},
year = {2005},
doi = {10.1534/genetics.104.037135},
abstract ={We introduce a stochastic model that describes neutral changes of gene expression over evolutionary time as a compound Poisson process where evolutionary events cause changes of expression level according to a given probability distribution. The model produces simple estimators for model parameters and allows discrimination between symmetric and asymmetric distributions of evolutionary expression changes along an evolutionary lineage. Furthermore, we introduce two measures, the skewness of expression difference distributions and relative difference of evolutionary branch lengths, which are used to quantify deviation from clock-like behavior of gene expression distances. Model-based analyses of gene expression profiles in primate liver and brain samples yield the following results: (1) The majority of gene expression changes are consistent with a neutral model of evolution; (2) along evolutionary lineages, upward changes in expression are less frequent but of greater average magnitude than downward changes; and (3) the skewness measure and the relative branch length difference confirm that an acceleration of gene expression evolution occurred on the human lineage in brain but not in liver. We discuss the latter result with respect to a neutral model of transcriptome evolution and show that a small number of genes expressed in brain can account for the observed data.},
URL = {http://www.genetics.org/content/170/2/929.abstract},
eprint = {http://www.genetics.org/content/170/2/929.full.pdf+html},
journal = {Genetics}
}
}
@book{Simpson1944,
	Author = {George Gaylord Simpson},
	Optaddress = {*},
	Optannote = {*},
	Optedition = {*},
	Optkey = {*},
	Optmonth = {*},
	Optnote = {*},
	Optnumber = {*},
	Optseries = {*},
	Optvolume = {*},
	Publisher = {Columbia University Press},
	Title = {Tempo and Mode of Evolution},
	Year = {1944}}

@book{Simpson1953,
	Author = {George Gaylord Simpson},
	Optaddress = {*},
	Optannote = {*},
	Optedition = {*},
	Optkey = {*},
	Optmonth = {*},
	Optnote = {*},
	Optnumber = {*},
	Optseries = {*},
	Optvolume = {*},
	Publisher = {Columbia University Press},
	Title = {Tempo and Mode of Evolution},
	Year = {1953}}

@Manual{Rcore2013,
   title = {R: A Language and Environment for Statistical Computing},
   author = {{R Core Team}},
   organization = {R Foundation for Statistical Computing},
   address = {Vienna, Austria},
   year = {2014},
   url = {http://www.R-project.org/},
}
@article{Hansen1997,
	Abstract = {Comparative studies tend to differ from optimality and functionality studies in how they treat adaptation. While the comparative approach focuses on the origin and change of traits, optimality studies assume that adaptations are maintained at an optimum by stabilizing selection. This paper presents a model of adaptive evolution on a macroevolutionary time scale that includes the maintenance of traits at adaptive optima by stabilizing selection as the dominant evolutionary force. Interspecific variation is treated as variation in the position of adaptive optima. The model illustrates how phylogenetic constraints not only lead to correlations between phylogenetically related species, but also to imperfect adaptations. From this model, a statistical comparative method is derived that can be used to estimate the effect of a selective factor on adaptive optima in a way that would be consistent with an optimality study of adaptation to this factor. The method is illustrated with an analysis of dental evolution in fossil horses. The use of comparative methods to study evolutionary trends is also discussed.},
	Author = {Hansen, Thomas F.},
	Journal = {Evolution},
	Number = {5},
	Pages = {1341--1351},
	Title = {Stabilizing Selection and the Comparative Analysis of Adaptation},
	Volume = {51},
	Year = {1997}}

@InCollection{Hansen2012,
author = {Hansen, Thomas F},
title = {Adaptive Landscapes and Macroevolutionary Dynamics},
booktitle = {The Adaptive Landscape in Evolutionary Biology},
OPTcrossref = {•},
OPTkey = {•},
pages = {205--221},
publisher = {Oxford University Press},
year = {2012},
editor = {Svensson, Erik and Calsbeek, Ryan},
OPTvolume = {•},
OPTnumber = {•},
OPTseries = {•},
OPTtype = {•},
OPTchapter = {•},
OPTaddress = {•},
OPTedition = {•},
OPTmonth = {•},
OPTnote = {•},
OPTannote = {•}
}

@Book{Nosil2012,
author = {Nosil, Patrik},
ALTeditor = {•},
title = {Ecological Speciation},
publisher = {Oxford University Press},
year = {2012},
OPTkey = {•},
OPTvolume = {•},
OPTnumber = {•},
OPTseries = {•},
OPTaddress = {•},
OPTedition = {•},
OPTmonth = {•},
OPTnote = {•},
OPTannote = {•}
}

@article{JC1999,
title = "Tempo and mode of speciation in the sea ",
journal = "Trends in Ecology \& Evolution ",
volume = "14",
number = "2",
pages = "72--77",
year = "1999",
note = "",
issn = "0169-5347",
doi = "10.1016/S0169-5347(98)01504-3",
url = "http://www.sciencedirect.com/science/article/pii/S0169534798015043",
author = "Jeremy B.C. Jackson and Alan H. Cheetham",
keywords = "species",
keywords = "speciation",
keywords = "macroevolution",
keywords = "punctuated",
keywords = "equilibria",
keywords = "stasis",
keywords = "phylogeny",
keywords = "natural selection",
keywords = "life history evolution",
keywords = "evolutionary trends",
keywords = "marine evolution "
}

@article {Aze2011,
author = {Aze, Tracy and Ezard, Thomas H. G. and Purvis, Andy and Coxall, Helen K. and Stewart, Duncan R. M. and Wade, Bridget S. and Pearson, Paul N.},
title = {A phylogeny of {C}enozoic macroperforate planktonic foraminifera from fossil data},
journal = {Biological Reviews},
volume = {86},
number = {4},
publisher = {Blackwell Publishing Ltd},
issn = {1469-185X},
url = {http://dx.doi.org/10.1111/j.1469-185X.2011.00178.x},
doi = {10.1111/j.1469-185X.2011.00178.x},
pages = {900--927},
keywords = {planktonic foraminifera, macroevolution, Cenozoic, biodiversity, phylogeny, stratophenetics, morphospecies, speciation, extinction, pseudoextinction},
year = {2011},
}

@Article{Williamson1981,
author = {Williamson, P.G.},
title = {Palaeontological documentation of speciation in Cenozoic molluscs from Turkana Basin},
journal = {Nature},
year = {1981},
OPTkey = {•},
volume = {293},
OPTnumber = {•},
pages = {437--443},
OPTmonth = {•},
OPTnote = {•},
OPTannote = {•}
}

@article {VanBocxlaer2008,
author = {Van Bocxlaer, Bert and Damme, Dirk Van and Feibel, Craig S.},
title = {Gradual versus punctuated evolution in the {T}urkana {B}asin Molluscs: Evolutionary events or biological invasions?},
journal = {Evolution},
volume = {62},
number = {3},
publisher = {Blackwell Publishing Inc},
issn = {1558--5646},
url = {http://dx.doi.org/10.1111/j.1558-5646.2007.00296.x},
doi = {10.1111/j.1558-5646.2007.00296.x},
pages = {511--520},
keywords = {Biogeography, Kenya, palaeobiology, palaeohydrology, Plio-Pleistocene, stratigraphy},
year = {2008},
}

@article {Fryer1983,
author = {Fryer, G. and Greenwood, P.H. and Peake, J.F.},
title = {Punctuated equilibria, morphological stasis and the palaeontological documentation of speciation: a biological appraisal of a case history in an {A}frican lake},
journal = {Biological Journal of the Linnean Society},
volume = {20},
number = {2},
publisher = {Blackwell Publishing Ltd},
issn = {1095-8312},
url = {http://dx.doi.org/10.1111/j.1095-8312.1983.tb00363.x},
doi = {10.1111/j.1095-8312.1983.tb00363.x},
pages = {195--205},
keywords = {Speciation, morphological stasis, variation, punctuated equilibria, fossil molluscs, cichlid fishes, African lakes},
year = {1983},
}

@article{VendittiPagel2010,
title = "Speciation as an active force in promoting genetic evolution ",
journal = "Trends in Ecology \& Evolution ",
volume = "25",
number = "1",
pages = "14--20",
year = "2010",
note = "",
issn = "0169-5347",
doi = "10.1016/j.tree.2009.06.010",
url = "http://www.sciencedirect.com/science/article/pii/S0169534709002225",
author = "Chris Venditti and Mark Pagel"
}

@article{Adams2009,
author = {Adams, Dean C. and Berns, Chelsea M. and Kozak, Kenneth H. and Wiens, John J.},
title = {Are rates of species diversification correlated with rates of morphological evolution?},
volume = {276},
number = {1668},
pages = {2729--2738},
year = {2009},
doi = {10.1098/rspb.2009.0543},
abstract ={Some major evolutionary theories predict a relationship between rates of proliferation of new species (species diversification) and rates of morphological divergence between them. However, this relationship has not been rigorously tested using phylogeny-based approaches. Here, we test this relationship with morphological and phylogenetic data from 190 species of plethodontid salamanders. Surprisingly, we find that rates of species diversification and morphological evolution are not significantly correlated, such that rapid diversification can occur with little morphological change, and vice versa. We also find that most clades have undergone remarkably similar patterns of morphological evolution (despite extensive sympatry) and that those relatively novel phenotypes are not associated with rapid diversification. Finally, we find a strong relationship between rates of size and shape evolution, which has not been previously tested.},
URL = {http://rspb.royalsocietypublishing.org/content/276/1668/2729.abstract},
eprint = {http://rspb.royalsocietypublishing.org/content/276/1668/2729.full.pdf+html},
journal = {Proceedings of the Royal Society B: Biological Sciences}
}

@article {RaboskyAdams2010,
author = {Rabosky, Daniel L. and Adams, Dean C.},
title = {Rates of morphological evolution are correlated with species richness in salamanders},
journal = {Evolution},
volume = {66},
number = {6},
publisher = {Blackwell Publishing Inc},
issn = {1558-5646},
url = {http://dx.doi.org/10.1111/j.1558-5646.2011.01557.x},
doi = {10.1111/j.1558-5646.2011.01557.x},
pages = {1807--1818},
keywords = {Adaptive radiation, macroevolution, morphological evolution, phylogenetics, speciation},
year = {2012},
}

@article{Pagel1997,
	Author = {Pagel, Mark},
	Date-Added = {2012-09-18 14:50:24 -0400},
	Date-Modified = {2012-09-18 14:50:24 -0400},
	Doi = {10.1111/j.1463-6409.1997.tb00423.x},
	Issn = {1463-6409},
	Journal = {Zoologica Scripta},
	Number = {4},
	Pages = {331--348},
	Publisher = {Blackwell Publishing Ltd},
	Title = {Inferring evolutionary processes from phylogenies},
	Url = {http://dx.doi.org/10.1111/j.1463-6409.1997.tb00423.x},
	Volume = {26},
	Year = {1997},
	Bdsk-Url-1 = {http://dx.doi.org/10.1111/j.1463-6409.1997.tb00423.x}}
}

@article{Mooers1999,
	Author = {Mooers, Arne {\O}. and Vamosi,, Steven M. and Schluter, Dolph},
	Journal = {The American Naturalist},
	Number = {2},
	Pages = {249--259},
	Title = {Using Phylogenies to Test Macroevolutionary Hypotheses of Trait Evolution in Cranes (\textit{Gruinae}).},
	Volume = {154},
	Year = {1999}}

@article{Mattila2008,
author = {Mattila, Tiina M and Bokma, Folmer},
title = {Extant mammal body masses suggest punctuated equilibrium},
volume = {275},
number = {1648},
pages = {2195--2199},
year = {2008},
doi = {10.1098/rspb.2008.0354},
abstract ={Is gradual microevolutionary change within species simultaneously the source of macroevolutionary differentiation between species? Since its first publication, Darwin's original idea that phenotypic differences between species develop gradually over time, as the accumulation of small selection-induced changes in successive generations has been challenged by palaeontologists claiming that, instead, new species quickly acquire their phenotypes to remain virtually unchanged until going extinct again. This controversy, widely known as the ‘punctuated equilibrium’ debate, remained unresolved, largely owing to the difficulty of distinguishing biological species from fossil remains. We analysed body masses of 2143 existing mammal species on a phylogeny comprising 4510 (i.e. nearly all) extant species to estimate rates of gradual (anagenetic) and speciational (cladogenetic) evolution. Our Bayesian estimates from mammals as well as separate sub-clades such as primates and carnivores suggest that gradual evolution is responsible for only a small part of body size variation between mammal species.},
URL = {http://rspb.royalsocietypublishing.org/content/275/1648/2195.abstract},
eprint = {http://rspb.royalsocietypublishing.org/content/275/1648/2195.full.pdf+html},
journal = {Proceedings of the Royal Society B: Biological Sciences}
}

@article{Nee1992,
author = {Nee, S and Mooers, A {\O} and Harvey, P H},
title = {Tempo and mode of evolution revealed from molecular phylogenies},
volume = {89},
number = {17},
pages = {8322--8326},
year = {1992},
abstract ={The analysis of the tempo and mode of evolution has a strong tradition in paleontology. Recent advances in molecular phylogenetic reconstruction make it possible to complement this work by using data from extant species.},
URL = {http://www.pnas.org/content/89/17/8322.abstract},
eprint = {http://www.pnas.org/content/89/17/8322.full.pdf+html},
journal = {Proceedings of the National Academy of Sciences}
}

@Article{Nee1994,
author = {Nee, Sean and May, Robert M and Harvey, Paul H},
title = {The Reconstructed Evolutionary Process},
journal = {Philosophical Transactions of the Royal Society: Biological Sciences},
year = {1994},
OPTkey = {•},
volume = {344},
number = {1309},
pages = {305--311},
OPTmonth = {•},
OPTnote = {•},
OPTannote = {•}
}

@article{Nee2006,
     jstor_articletype = {research-article},
     title = {Birth-Death Models in Macroevolution},
     author = {Nee, Sean},
     journal = {Annual Review of Ecology, Evolution, and Systematics},
     jstor_issuetitle = {},
     volume = {37},
     number = {},
     jstor_formatteddate = {2006},
     pages = {1--17},
     url = {http://www.jstor.org/stable/30033824},
     ISSN = {1543592X},
     abstract = {Birth-death models, and their subsets-the pure birth and pure death models-have a long history of use for informing thinking about macroevolutionary patterns. Here we illustrate with examples the wide range of questions they have been used to address, including estimating and comparing rates of diversification of clades, investigating the "shapes" of clades, and some rather surprising uses such as estimating speciation rates from data that are not resolved below the level of the genus. The raw data for inference can be the fossil record or the molecular phylogeny of a clade, and we explore the similarites and differences in the behavior of the birth-death models when applied to these different forms of data.},
     language = {English},
     year = {2006},
     publisher = {Annual Reviews},
     copyright = {Copyright © 2006 Annual Reviews},
    }

@article{Purvis2008,
author = {Purvis, Andy},
title = {Phylogenetic Approaches to the Study of Extinction},
journal = {Annual Review of Ecology, Evolution, and Systematics},
volume = {39},
number = {1},
pages = {301--319},
year = {2008},
doi = {10.1146/annurev-ecolsys-063008-102010},

URL = {http://www.annualreviews.org/doi/abs/10.1146/annurev-ecolsys-063008-102010},
eprint = {http://www.annualreviews.org/doi/pdf/10.1146/annurev-ecolsys-063008-102010}
}

@article{Arnold1979,
  title={Indian {O}cean giant tortoises: their systematics and island adaptations},
  author={Arnold, E Nicholas},
  journal={Philosophical Transactions of the Royal Society of London. B, Biological Sciences},
  volume={286},
  number={1011},
  pages={127--145},
  year={1979},
  publisher={The Royal Society}
}

@article{Stone2011,
author = {Stone, Graham N. and Nee, Sean and Felsenstein, Joseph},
title = {Controlling for non-independence in comparative analysis of patterns across populations within species},
volume = {366},
number = {1569},
pages = {1410--1424},
year = {2011},
doi = {10.1098/rstb.2010.0311},
abstract ={How do we quantify patterns (such as responses to local selection) sampled across multiple populations within a single species? Key to this question is the extent to which populations within species represent statistically independent data points in our analysis. Comparative analyses across species and higher taxa have long recognized the need to control for the non-independence of species data that arises through patterns of shared common ancestry among them (phylogenetic non-independence), as have quantitative genetic studies of individuals linked by a pedigree. Analyses across populations lacking pedigree information fall in the middle, and not only have to deal with shared common ancestry, but also the impact of exchange of migrants between populations (gene flow). As a result, phenotypes measured in one population are influenced by processes acting on others, and may not be a good guide to either the strength or direction of local selection. Although many studies examine patterns across populations within species, few consider such non-independence. Here, we discuss the sources of non-independence in comparative analysis, and show why the phylogeny-based approaches widely used in cross-species analyses are unlikely to be useful in analyses across populations within species. We outline the approaches (intraspecific contrasts, generalized least squares, generalized linear mixed models and autoregression) that have been used in this context, and explain their specific assumptions. We highlight the power of ‘mixed models’ in many contexts where problems of non-independence arise, and show that these allow incorporation of both shared common ancestry and gene flow. We suggest what can be done when ideal solutions are inaccessible, highlight the need for incorporation of a wider range of population models in intraspecific comparative methods and call for simulation studies of the error rates associated with alternative approaches.},
URL = {http://rstb.royalsocietypublishing.org/content/366/1569/1410.abstract},
eprint = {http://rstb.royalsocietypublishing.org/content/366/1569/1410.full.pdf+html},
journal = {Philosophical Transactions of the Royal Society B: Biological Sciences}
}

@mastersthesis{Jialian2012,
	title= {Reversible Jump {M}arkov {C}hain {M}onte {C}arlo Methods},
	author= {Jialin, Ai},
	year= {2012},
	school= {University of Leeds},
}

@Article{Reitan2012,
author = {Reitan, Trond and Schweder, Tore and Henderiks, Jorijntje},
title = {Phenotypic evolution studied by layered stochastic differential equations},
journal = {Annals of Applied Statistics},
year = {2012},
OPTkey = {•},
volume = {6},
OPTnumber = {•},
pages = {1531--1551},
OPTmonth = {•},
OPTnote = {•},
OPTannote = {•}
}

@article{Lapiedra2013,
  title={Behavioural changes and the adaptive diversification of pigeons and doves},
  author={Lapiedra, Oriol and Sol, Daniel and Carranza, Salvador and Beaulieu, Jeremy M},
  journal={Proceedings of the Royal Society B: Biological Sciences},
  volume={280},
  number={1755},
  year={2013},
  publisher={The Royal Society}
}

@article{IngramMahler2013,
  title={{SURFACE}: detecting convergent evolution from comparative data by fitting {O}rnstein-{U}hlenbeck models with stepwise {A}kaike {I}nformation {C}riterion},
  author={Ingram, Travis and Mahler, D Luke},
  journal={Methods in Ecology and Evolution},
  year={2013},
  publisher={Wiley Online Library}
}

@article{Mahler2013,
  title={Exceptional Convergence on the Macroevolutionary Landscape in Island Lizard Radiations},
  author={Mahler, D Luke and Ingram, Travis and Revell, Liam J and Losos, Jonathan B},
  journal={Science},
  volume={341},
  number={6143},
  pages={292--295},
  year={2013},
  publisher={American Association for the Advancement of Science}
}

@article{Eldredge2005,
     jstor_articletype = {research-article},
     title = {The Dynamics of Evolutionary Stasis},
     author = {Eldredge, Niles and Thompson, John N. and Brakefield, Paul M. and Gavrilets, Sergey and Jablonski, David and Jackson, Jeremy B. C. and Lenski, Richard E. and Lieberman, Bruce S. and McPeek, Mark A. and Miller, William, III},
     journal = {Paleobiology},
     jstor_issuetitle = {Supplement. Macroevolution: Diversity, Disparity, Contingency: Essays in Honor of Stephen Jay Gould},
     volume = {31},
     number = {2},
     jstor_formatteddate = {Spring, 2005},
     pages = {133--145},
     url = {http://www.jstor.org/stable/25482674},
     ISSN = {00948373},
     abstract = {The fossil record displays remarkable stasis in many species over long time periods, yet studies of extant populations often reveal rapid phenotypic evolution and genetic differentiation among populations. Recent advances in our understanding of the fossil record and in population genetics and evolutionary ecology point to the complex geographic structure of species being fundamental to resolution of how taxa can commonly exhibit both short-term evolutionary dynamics and long-term stasis.},
     language = {English},
     year = {2005},
     publisher = {Paleontological Society},
     copyright = {Copyright © 2005 Paleontological Society},
    }

@article {Saetre2013,
author = {S{\ae}tre, G.-P.},
title = {Hybridization is important in evolution, but is speciation?},
journal = {Journal of Evolutionary Biology},
volume = {26},
number = {2},
issn = {1420-9101},
url = {http://dx.doi.org/10.1111/jeb.12005},
doi = {10.1111/jeb.12005},
pages = {256--258},
year = {2013},
}

@Book{Mayr,
author = {Mayr, Ernst},
ALTeditor = {•},
title = {Systematics and the Origin of Species from the Viewpoint of a Zoologist},
publisher = {Harvard University Press},
year = {1942},
OPTkey = {•},
OPTvolume = {•},
OPTnumber = {•},
OPTseries = {•},
OPTaddress = {•},
OPTedition = {•},
OPTmonth = {•},
OPTnote = {•},
OPTannote = {•}
}

@article{Futuyma1987,
     jstor_articletype = {research-article},
     title = {On the Role of Species in Anagenesis},
     author = {Futuyma, Douglas J.},
     journal = {The American Naturalist},
     jstor_issuetitle = {},
     volume = {130},
     number = {3},
     jstor_formatteddate = {Sep., 1987},
     pages = {465--473},
     url = {http://www.jstor.org/stable/2461899},
     ISSN = {00030147},
     abstract = {},
     language = {English},
     year = {1987},
     publisher = {The University of Chicago Press for The American Society of Naturalists},
     copyright = {Copyright © 1987 The University of Chicago},
    }

@article{GouldVrba1986,
     jstor_articletype = {research-article},
     title = {The Hierarchical Expansion of Sorting and Selection: Sorting and Selection Cannot Be Equated},
     author = {Vrba, Elisabeth S. and Gould, Stephen Jay},
     journal = {Paleobiology},
     jstor_issuetitle = {},
     volume = {12},
     number = {2},
     jstor_formatteddate = {Spring, 1986},
     pages = {217--228},
     url = {http://www.jstor.org/stable/2400492},
     ISSN = {00948373},
     abstract = {In a nonhierarchical world, where selection on organisms regulated all nonrandom evolutionary change, the traditional equation of selection (a cause of sorting) with sorting itself (differential birth and death among varying organisms within a population) would rarely lead to error, even though the phenomena are logically distinct (for sorting is a simple description of differential "success," and selection a causal process). But in a hierarchical world, with entities acting as evolutionary individuals (genes, organisms, and species among them) at several levels of ascending inclusion, sorting among entities at one level has a great range of potential causes. Direct selection upon entities themselves is but one possibility among many. This paper discusses why hierarchy demands that sorting and selection be disentangled. It then presents and illustrates an expanded taxonomy of sorting for a hierarchical world. For each of three levels (genes, organisms, and species), we show how sorting can arise from selection at the focal level itself, and as a consequence either of downward causation from processes acting on individuals at higher levels or upward causation from lower levels. We then discuss how hierarchy might illuminate a range of evolutionary questions based on both the logical structure of hierarchy and the historical pathways of its construction-for hierarchy is a property of nature, not only a conceptual scheme for organization.},
     language = {English},
     year = {1986},
     publisher = {Paleontological Society},
     copyright = {Copyright © 1986 Paleontological Society},
    }

@article{Turner2010,
year={2010},
issn={1431-7613},
journal={Theory in Biosciences},
volume={129},
number={2-3},
doi={10.1007/s12064-010-0088-6},
title={Punctuated equilibrium and species selection: what does it mean for one theory to suggest another?},
url={http://dx.doi.org/10.1007/s12064-010-0088-6},
publisher={Springer-Verlag},
keywords={Fossil record; Punctuated equilibrium; Species selection; Theoretical fertility},
author={Turner, Derek},
pages={113--123},
language={English}
}

@Book{Dennett1995,
author = {Dennett, Daniel C.},
ALTeditor = {•},
title = {Darwin's Dangerous Idea: Evolution and the meanings of life},
publisher = {Simon \& Schuster},
year = {1995},
OPTkey = {•},
OPTvolume = {•},
OPTnumber = {•},
OPTseries = {•},
OPTaddress = {•},
OPTedition = {•},
OPTmonth = {•},
OPTnote = {•},
OPTannote = {•}
}

@article{Bookstein1978,
     jstor_articletype = {research-article},
     title = {Hierarchical Linear Modeling of the Tempo and Mode of Evolution},
     author = {Bookstein, Fred L. and Gingerich, Philip D. and Kluge, Arnold G.},
     journal = {Paleobiology},
     jstor_issuetitle = {},
     volume = {4},
     number = {2},
     jstor_formatteddate = {Spring, 1978},
     pages = {120--134},
     url = {http://www.jstor.org/stable/2400281},
     ISSN = {00948373},
     abstract = {Punctuated equilibrium and phyletic gradualism are alternative hypotheses that purport to explain the tempo and mode of evolution. We evaluate the two hypotheses, as they apply to the fossil record, on both theoretical and empirical grounds. Hidden randomness in data increases as a function of greater aggregation, and the hypothesis of punctuated equilibrium should not be applied to those examples where randomness is likely to occur. False stasis can result from a sustained pattern of emigration and immigration, and geographic variation must be studied in order to posit an unambiguous case of punctuated equilibrium. We describe a statistical method based on the general linear model for testing the relative fit of the alternative hypotheses to any set of temporally ordered metric data. Our method is hierarchical in the sense that subsets of the total explained variance can themselves be explained. The size of the first molar of the primate Pelycodus and of the condylarth Hyopsodus are analyzed. There are 17 tests in the two data sets, and we discover 12 instances of gradualism, four of punctuation and one of equilibrium.},
     language = {English},
     year = {1978},
     publisher = {Paleontological Society},
     copyright = {Copyright © 1978 Paleontological Society},
    }

@article{Slatkin1981,
     jstor_articletype = {research-article},
     title = {A Diffusion Model of Species Selection},
     author = {Slatkin, Montgomery},
     journal = {Paleobiology},
     jstor_issuetitle = {},
     volume = {7},
     number = {4},
     jstor_formatteddate = {Autumn, 1981},
     pages = {421--425},
     url = {http://www.jstor.org/stable/2400693},
     ISSN = {00948373},
     abstract = {A diffusion model of the distribution of a phenotypic character in a group of species is developed and analyzed. The model incorporates the combined effects of phyletic evolution, speciation and extinction. Directed speciation is modeled by assuming there is some bias to phenotypic changes during speciation. Species selection is modeled by assuming there is some dependence of either speciation or extinction rates on the phenotypic character. Three examples are analyzed to illustrate the use of the model. A model of completely random changes due to both phyletic evolution and speciation shows how between-species differences are established. A model of directed speciation due to multiplicative changes during speciation shows how a simple assumption about the speciation process can produce macroevolutionary trends. A model of species selection due to differences in extinction rates shows how the efficacy of species selection depends on the between-species variance produced both by speciation and by phyletic evolution.},
     language = {English},
     year = {1981},
     publisher = {Paleontological Society},
     copyright = {Copyright © 1981 Paleontological Society},
    }

@article{ArnoldFristrup1982,
     jstor_articletype = {research-article},
     title = {The Theory of Evolution by Natural Selection: A Hierarchical Expansion},
     author = {Arnold, Anthony J. and Fristrup, Kurt},
     journal = {Paleobiology},
     jstor_issuetitle = {},
     volume = {8},
     number = {2},
     jstor_formatteddate = {Spring, 1982},
     pages = {113--129},
     url = {http://www.jstor.org/stable/2400448},
     ISSN = {00948373},
     abstract = {Alleles, individuals, and species are all examples of entities possessing variation in the properties that underlie natural selection: branching (reproduction), persistence (survivorship), and heritability of characters. This suggests that the logic embodied in the theory of natural selection can be abstracted from its usual application to the level of individuals to encompass selection operating among any biological entities for which these essential properties can be meaningfully defined. This approach leads to a unified perspective of adaptation, selection, and fitness at all levels. Expanded versions of the Price covariance selection equations provide a convenient and useful conceptual vehicle for this discussion. The advantages of a hierarchical approach are twofold: it permits exploration of concepts and ideas across levels by analogy, and it focuses attention upon the mechanisms that account for different evolutionary dynamics at each level rather than obscuring these biologically unique properties with argument by extension from a single "special" level. We point out that the choice of a single measure of evolutionary change restricts the context in which "other level" processes will be perceived. We illustrate the limited forms in which higher and lower level selection can be recognized from the unique perspective provided by any given level through extensions of Price's formula. An exploration of the implications of such an approach leads us to the assertion that the development of a unified theory of evolution demands the recognition and incorporation of hierarchical structure as a conceptual foundation.},
     language = {English},
     year = {1982},
     publisher = {Paleontological Society},
     copyright = {Copyright © 1982 Paleontological Society},
    }

@article{Rice1995,
title = "A Genetical Theory of Species Selection ",
journal = "Journal of Theoretical Biology ",
volume = "177",
number = "3",
pages = "237--245",
year = "1995",
note = "",
issn = "0022-5193",
doi = "10.1006/jtbi.1995.0241",
url = "http://www.sciencedirect.com/science/article/pii/S002251938570241X",
author = "Sean H. Rice"
}

@article{McShea2004,
year={2004},
issn={0169-3867},
journal={Biology and Philosophy},
volume={19},
number={1},
doi={10.1023/B:BIPH.0000013260.40162.dd},
title={A Revised Darwinism},
url={http://dx.doi.org/10.1023/B%3ABIPH.0000013260.40162.dd},
publisher={Kluwer Academic Publishers},
author={McShea, DanielW.},
pages={45--53},
language={English}
}

@article{Sargent2004,
author = {Sargent, Risa D.},
title = {Floral symmetry affects speciation rates in angiosperms},
volume = {271},
number = {1539},
pages = {603--608},
year = {2004},
doi = {10.1098/rspb.2003.2644},
abstract ={Despite much recent activity in the field of pollination biology, the extent to which animal pollinators drive the formation of new angiosperm species remains unresolved. One problem has been identifying floral adaptations that promote reproductive isolation. The evolution of a bilaterally symmetrical corolla restricts the direction of approach and movement of pollinators on and between flowers. Restricting pollinators to approaching a flower from a single direction facilitates specific placement of pollen on the pollinator. When coupled with pollinator constancy, precise pollen placement can increase the probability that pollen grains reach a compatible stigma. This has the potential to generate reproductive isolation between species, because mutations that cause changes in the placement of pollen on the pollinator may decrease gene flow between incipient species. I predict that animal‚Äìpollinated lineages that possess bilaterally symmetrical flowers should have higher speciation rates than lineages possessing radially symmetrical flowers. Using sister‚Äìgroup comparisons I demonstrate that bilaterally symmetric lineages tend to be more species rich than their radially symmetrical sister lineages. This study supports an important role for pollinator‚Äìmediated speciation and demonstrates that floral morphology plays a key role in angiosperm speciation.},
URL = {http://rspb.royalsocietypublishing.org/content/271/1539/603.abstract},
eprint = {http://rspb.royalsocietypublishing.org/content/271/1539/603.full.pdf+html},
journal = {Proceedings of the Royal Society of London. Series B: Biological Sciences}
}

@article {Vamosi2004,
author = {Vamosi, Jana C. and Vamosi, Steven M.},
title = {The Role of Diversification in Causing the Correlates of Dioecy},
journal = {Evolution},
volume = {58},
number = {4},
publisher = {Blackwell Publishing Ltd},
issn = {1558-5646},
url = {http://dx.doi.org/10.1111/j.0014-3820.2004.tb00405.x},
doi = {10.1111/j.0014-3820.2004.tb00405.x},
pages = {723--731},
keywords = {Angiosperms, breeding system, dioecy, ecological correlations, extinction, phylogeny, sister-group comparison, speciation},
year = {2004},
}

@article{Slowinski1989,
   author = {Slowinski, J. B. and Guyer, C.},
   title = {Testing the Stochasticity of Patterns of Organismal Diversity - An Improved Null Model},
   journal = {American Naturalist},
   volume = {134},
   number = {6},
   pages = {907--921},
   year = {1989}
}

@article{Slowinski1993,
   author = {Slowinski, J. B. and Guyer, C.},
   title = {Testing Whether Certain Traits Have Caused Amplified Diversification - An Improved Method Based on a Model of Random Speciation and Extinction},
   journal = {American Naturalist},
   volume = {142},
   number = {6},
   pages = {1019--1024},
   year = {1993}
}

@Article{VamosiVamosi,
author = {Vamosi, Steven M. and Vamosi, Jana C.},
title = {Endless tests: guidelines for analysing non-nested sister-group comparisons},
journal = {Evolutionary Ecology Research},
year = {2005},
OPTkey = {•},
volume = {7},
OPTnumber = {•},
pages = {657--579},
OPTmonth = {•},
OPTnote = {•},
OPTannote = {•}
}

@article {Maddison2006,
author = {Maddison, Wayne P.},
title = {Confounding Asymmetries in Evolution Diversification and Character Change},
journal = {Evolution},
volume = {60},
number = {8},
publisher = {Blackwell Publishing Ltd},
issn = {1558-5646},
url = {http://dx.doi.org/10.1111/j.0014-3820.2006.tb00517.x},
doi = {10.1111/j.0014-3820.2006.tb00517.x},
pages = {1743--1746},
keywords = {Diversification, evolutionary dead-end, extinction, irreversibility, phylogeny, speciation},
year = {2006},
}

@article{Goldberg2011,
author = {Goldberg, Emma E. and Lancaster, Lesley T. and Ree, Richard H.},
title = {Phylogenetic Inference of Reciprocal Effects between Geographic Range Evolution and Diversification},
volume = {60},
number = {4},
pages = {451--465},
year = {2011},
doi = {10.1093/sysbio/syr046},
abstract ={Geographic characters‚Äîtraits describing the spatial distribution of a species‚Äîmay both affect and be affected by processes associated with lineage birth and death. This is potentially confounding to comparative analyses of species distributions because current models do not allow reciprocal interactions between the evolution of ranges and the growth of phylogenetic trees. Here, we introduce a likelihood-based approach to estimating region-dependent rates of speciation, extinction, and range evolution from a phylogeny, using a new model in which these processes are interdependent. We demonstrate the method with simulation tests that accurately recover parameters relating to the mode of speciation and source‚Äìsink dynamics. We then apply it to the evolution of habitat occupancy in Californian plant communities, where we find higher rates of speciation in chaparral than in forests and evidence for expanding habitat tolerances.},
URL = {http://sysbio.oxfordjournals.org/content/60/4/451.abstract},
eprint = {http://sysbio.oxfordjournals.org/content/60/4/451.full.pdf+html},
journal = {Systematic Biology}
}

@article{QuentalMarshall2010,
   author = {Quental, T. B. and Marshall, C. R.},
   title = {Diversity dynamics: molecular phylogenies need the fossil record},
   journal = {Trends in Ecology \& Evolution},
   volume = {25},
   number = {8},
   pages = {434--441},
   abstract = {Over the last two decades, new tools in the analysis of molecular phylogenies have enabled study of the diversification dynamics of living clades in the absence of information about extinct lineages. However, computer simulations and the fossil record show that the inability to access extinct lineages severely limits the inferences that can be drawn from molecular phylogenies. It appears that molecular phylogenies can tell us only when there have been changes in diversification rates, but are blind to the true diversity trajectories and rates of origination and extinction that have led to the species that are alive today. We need to embrace the fossil record if we want to fully understand the diversity dynamics of the living biota.},
   year = {2010}
}

@article{Akaike1974,
	Author = {Akaike, H.},
	Doi = {10.1109/TAC.1974.1100705},
	Journal = {Automatic Control, IEEE Transactions on},
	Month = {dec},
	Number = {6},
	Pages = {716--723},
	Title = {A new look at the statistical model identification},
	Volume = {19},
	Year = {1974},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/TAC.1974.1100705}}

@article{ButlerKing2004,
	Abstract = {Abstract: Biologists employ phylogenetic comparative methods to study adaptive evolution. However, none of the popular methods model selection directly. We explain and develop a method based on the Ornstein‐Uhlenbeck (OU) process, first proposed by Hansen. Ornstein‐Uhlenbeck models incorporate both selection and drift and are thus qualitatively different from, and more general than, pure drift models based on Brownian motion. Most importantly, OU models possess selective optima that formalize the notion of adaptive zone. In this article, we develop the method for one quantitative character, discuss interpretations of its parameters, and provide code implementing the method. Our approach allows us to translate hypotheses regarding adaptation in different selective regimes into explicit models, to test the models against data using maximum‐likelihood‐based model selection techniques, and to infer details of the evolutionary process. We illustrate the method using two worked examples. Relative to existing approaches, the direct modeling approach we demonstrate allows one to explore more detailed hypotheses and to utilize more of the information content of comparative data sets than existing methods. Moreover, the use of a model selection framework to simultaneously compare a variety of hypotheses advances our ability to assess alternative evolutionary explanations.},
	Author = {Butler, Marguerite A. and King, Aaron A.},
	Journal = {The American Naturalist},
	Number = {6},
	Pages = {683--695},
	Title = {Phylogenetic Comparative Analysis: A Modeling Approach for Adaptive Evolution.},
	Volume = {164},
	Year = {2004}}	}

@Article{SimpsonHarnik2009,
author = {Simpson, Carl and Harnik, Paul G.},
title = {Assessing the role fo abundance in marine bivalve extinction over the Post-{P}aleozoic},
journal = {Paleobiology},
year = {2009},
OPTkey = {•},
volume = {35},
OPTnumber = {•},
pages = {631--647},
OPTmonth = {•},
OPTnote = {•},
OPTannote = {•}
}

@Article{Simpson2010,
author = {Simpson, Carl},
title = {Species selection and driven mechanisms jointly generate a large-scale morphological trend in monobathrid crnioids},
journal = {Paleobiology},
year = {2010},
OPTkey = {•},
volume = {36},
OPTnumber = {•},
pages = {481--496},
OPTmonth = {•},
OPTnote = {•},
OPTannote = {•}
}

@Article{Goldie2011,
author = {Goldie, Xavier and Lanfear, Robert and Bromham, Lindell},
title = {Diversification and the rate of molecular evolution: no evidence of a link in mammals},
journal = {BMC Evolutionary Biology},
year = {2011},
OPTkey = {•},
volume = {11},
OPTnumber = {•},
pages = {286},
OPTmonth = {•},
OPTnote = {•},
OPTannote = {•}
}

@article {Rundle2005,
author = {Rundle, Howard D. and Nosil, Patrik},
title = {Ecological speciation},
journal = {Ecology Letters},
volume = {8},
number = {3},
publisher = {Blackwell Science Ltd},
issn = {1461-0248},
url = {http://dx.doi.org/10.1111/j.1461-0248.2004.00715.x},
doi = {10.1111/j.1461-0248.2004.00715.x},
pages = {336--352},
keywords = {Divergent selection, natural selection, reinforcement, reproductive isolation, sexual selection},
year = {2005},
}

@article{Head2009,
  title={Giant boid snake from the {P}alaeocene neotropics reveals hotter past equatorial temperatures},
  author={Head, Jason J and Bloch, Jonathan I and Hastings, Alexander K and Bourque, Jason R and Cadena, Edwin A and Herrera, Fabiany A and Polly, P David and Jaramillo, Carlos A},
  journal={Nature},
  volume={457},
  number={7230},
  pages={715--717},
  year={2009},
  publisher={Nature Publishing Group}
}

@article{Makarieva2005,
  title={Gigantism, Temperature and Metabolic Rate in Terrestrial Poikilotherms},
  author={Makarieva, Anastassia M and Gorshkov, Victor G and Li, Bai-Lian},
  journal={Proceedings: Biological Sciences},
  pages={2325--2328},
  year={2005},
  publisher={JSTOR}
}

@article{Rohlfs2013,
  title={Modeling gene expression evolution with an extended Ornstein-Uhlenbeck process accounting for within-species variation},
  author={Rohlfs, Rori V and Harrigan, Patrick and Nielsen, Rasmus},
  journal={Molecular biology and evolution},
  pages={mst190},
  year={2013},
  publisher={SMBE}
}

@article{Huelsenbeck2004,
  title={Bayesian phylogenetic model selection using reversible jump {M}arkov chain {M}onte {C}arlo},
  author={Huelsenbeck, John P and Larget, Bret and Alfaro, Michael E},
  journal={Molecular biology and evolution},
  volume={21},
  number={6},
  pages={1123--1133},
  year={2004},
  publisher={SMBE}
}

@article{Huelsenbeck2000,
  title={A compound {P}oisson process for relaxing the molecular clock},
  author={Huelsenbeck, John P and Larget, Bret and Swofford, David},
  journal={Genetics},
  volume={154},
  number={4},
  pages={1879--1892},
  year={2000},
  publisher={Genetics Soc America}
}

@article{Kimura1980,
  title={A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences},
  author={Kimura, Motoo},
  journal={Journal of molecular evolution},
  volume={16},
  number={2},
  pages={111--120},
  year={1980},
  publisher={Springer}
}

@book{Kimura1984,
  title={The neutral theory of molecular evolution},
  author={Kimura, Motoo},
  year={1984},
  publisher={Cambridge University Press}
}

@article{Felsenstein1981,
  title={Evolutionary trees from {DNA} sequences: a maximum likelihood approach},
  author={Felsenstein, Joseph},
  journal={Journal of molecular evolution},
  volume={17},
  number={6},
  pages={368--376},
  year={1981},
  publisher={Springer}
}

@article{Hunt2013,
  title={Testing the link between phenotypic evolution and speciation: an integrated palaeontological and phylogenetic analysis},
  author={Hunt, Gene},
  journal={Methods in Ecology and Evolution},
  volume={4},
  number={8},
  pages={714--723},
  year={2013},
  publisher={Wiley Online Library}
}

@article{Pienaar2013,
  title={Macroevolution of life-history traits in passerine birds: adaptation and phylogenetic inertia},
  author={Pienaar, Jason and Ilany, Amiyaal and Geffen, Eli and Yom-Tov, Yoram},
  journal={Ecology letters},
  year={2013},
  publisher={Wiley Online Library}
}

@article{Escudero2012,
  title={Selection and inertia in the evolution of holocentric chromosomes in sedges (textit{Carex}, {C}yperaceae)},
  author={Escudero, Marcial and Hipp, Andrew L and Hansen, Thomas F and Voje, Kjetil L and Luce{\~n}o, Modesto},
  journal={New Phytologist},
  volume={195},
  number={1},
  pages={237--247},
  year={2012},
  publisher={Wiley Online Library}
}

@article{Bartoszek2012,
title = "A phylogenetic comparative method for studying multivariate adaptation ",
journal = "Journal of Theoretical Biology ",
volume = "314",
number = "0",
pages = "204--215",
year = "2012",
note = "",
issn = "0022-5193",
doi = "10.1016/j.jtbi.2012.08.005",
url = "http://www.sciencedirect.com/science/article/pii/S0022519312003918",
author = "Krzysztof Bartoszek and Jason Pienaar and Petter Mostad and Staffan Andersson and Thomas F. Hansen",
keywords = "Ornstein–Uhlenbeck process",
keywords = "Multivariate phylogenetic comparative method",
keywords = "Adaptation",
keywords = "Optimality",
keywords = "Allometry "
}

@article{Pennell2013,
  title={Is there room for punctuated equilibrium in macroevolution?},
  author={Pennell, Matthew W and Harmon, Luke J and Uyeda, Josef C},
  journal={Trends in ecology \& evolution},
  year={2013},
  publisher={Elsevier}
}

@article {Hansen2008,
author = {Hansen, Thomas F. and Pienaar, Jason and Orzack, Steven Hecht},
title = {A Comparative Method for Stuyding Adaptation to a Randomly Evolving Environment},
journal = {Evolution},
volume = {62},
number = {8},
publisher = {Blackwell Publishing Inc},
issn = {1558--5646},
url = {http://dx.doi.org/10.1111/j.1558-5646.2008.00412.x},
doi = {10.1111/j.1558-5646.2008.00412.x},
pages = {1965--1977},
keywords = {Adaptation, maladaptation, optimality, Ornstein–Uhlenbeck process, phylogenetic comparative method, phylogenetic effect, phylogenetic inertia},
year = {2008},
}

@article{Hansen2012b,
author = {Hansen, Thomas F. and Bartoszek, Krzysztof},
title = {Interpreting the Evolutionary Regression: The Interplay Between Observational and Biological Errors in Phylogenetic Comparative Studies},
volume = {61},
number = {3},
pages = {413--425},
year = {2012},
doi = {10.1093/sysbio/syr122},
abstract ={Regressions of biological variables across species are rarely perfect. Usually, there are residual deviations from the estimated model relationship, and such deviations commonly show a pattern of phylogenetic correlations indicating that they have biological causes. We discuss the origins and effects of phylogenetically correlated biological variation in regression studies. In particular, we discuss the interplay of biological deviations with deviations due to observational or measurement errors, which are also important in comparative studies based on estimated species means. We show how bias in estimated evolutionary regressions can arise from several sources, including phylogenetic inertia and either observational or biological error in the predictor variables. We show how all these biases can be estimated and corrected for in the presence of phylogenetic correlations. We present general formulas for incorporating measurement error in linear models with correlated data. We also show how alternative regression models, such as major axis and reduced major axis regression, which are often recommended when there is error in predictor variables, are strongly biased when there is biological variation in any part of the model. We argue that such methods should never be used to estimate evolutionary or allometric regression slopes.},
URL = {http://sysbio.oxfordjournals.org/content/61/3/413.abstract},
eprint = {http://sysbio.oxfordjournals.org/content/61/3/413.full.pdf+html},
journal = {Systematic Biology}
}

@InCollection{WagnerErwin1995,
author = {Wagner, Peter J. and Erwin, Douglas H.},
title = {Phylogenetic patterns as tests of speciation models},
booktitle = {New Approaches to Speciation in the Fossil Record},
OPTcrossref = {•},
OPTkey = {•},
pages = {87--122},
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{Hunt2008,
author = {Hunt, Gene},
title = {Gradual or pulsed evolution: when should punctuational explanations be preferred?},
journal = {Paleobiology},
year = {2008},
OPTkey = {•},
volume = {34},
OPTnumber = {•},
pages = {360--377},
OPTmonth = {•},
OPTnote = {•},
OPTannote = {•}
}

@article{Webster2003,
author = {Webster, Andrea J. and Payne, Robert J. H. and Pagel, Mark},
title = {Molecular Phylogenies Link Rates of Evolution and Speciation},
volume = {301},
number = {5632},
pages = {478},
year = {2003},
doi = {10.1126/science.1083202},
URL = {http://www.sciencemag.org/content/301/5632/478.short},
eprint = {http://www.sciencemag.org/content/301/5632/478.full.pdf},
journal = {Science}
}

@Book{Williams1992,
author = {Williams, George C.},
ALTeditor = {•},
title = {Natural Selection: Domains, Levels and Challenges},
publisher = {Oxford University Press},
year = {1992},
OPTkey = {•},
OPTvolume = {•},
OPTnumber = {•},
OPTseries = {•},
OPTaddress = {•},
OPTedition = {•},
OPTmonth = {•},
OPTnote = {•},
OPTannote = {•}
}

@Book{Levinton2001,
author = {Levinton, Jeffrey S.},
ALTeditor = {•},
title = {Genetics, Paleontology and Macroevolution},
publisher = {Cambridge University Press},
year = {2001},
OPTkey = {•},
OPTvolume = {•},
OPTnumber = {•},
OPTseries = {•},
OPTaddress = {•},
OPTedition = {•},
OPTmonth = {•},
OPTnote = {•},
OPTannote = {•}
}

@Book{Rice2004,
author = {Rice, Sean H.},
ALTeditor = {•},
title = {Evolutionary Theory},
publisher = {Sinauer and Associates},
year = {2004},
OPTkey = {•},
OPTvolume = {•},
OPTnumber = {•},
OPTseries = {•},
OPTaddress = {•},
OPTedition = {•},
OPTmonth = {•},
OPTnote = {•},
OPTannote = {•}
}

@Book{Sepkoskibook,
author = {Sepkoski, David},
ALTeditor = {•},
title = {Rereading the Fossil Record: The Growth of Paleobiology and an Evolutionary Discripline},
publisher = {University of Chicago Press},
year = {2012},
OPTkey = {•},
OPTvolume = {•},
OPTnumber = {•},
OPTseries = {•},
OPTaddress = {•},
OPTedition = {•},
OPTmonth = {•},
OPTnote = {•},
OPTannote = {•}
}

@Article{Mayr1982,
author = {Mayr, Ernst},
title = {Speciation and Macroevolution},
journal = {Evolution},
year = {1982},
OPTkey = {•},
volume = {36},
OPTnumber = {•},
pages = {1119--1132},
OPTmonth = {•},
OPTnote = {•},
OPTannote = {•}
}

@InCollection{Ruse1989,
author = {Ruse, Michael},
title = {Is the Theory of Punctuated Equilibria a New Paradigm?},
booktitle = {The Darwinian Paradigm},
OPTcrossref = {•},
OPTkey = {•},
OPTpages = {•},
publisher = {Harvard University Press},
year = {1989},
editor = {Ruse, Michael},
OPTvolume = {•},
OPTnumber = {•},
OPTseries = {•},
OPTtype = {•},
OPTchapter = {•},
OPTaddress = {•},
OPTedition = {•},
OPTmonth = {•},
OPTnote = {•},
OPTannote = {•}
}

@Article{Houle2011,
author = {Houle, D. and P\'{e}labon C. and Wagner, G.P. and Hansen, T.F.},
title = {Measurement and meaning in biology},
journal = {Quarterly Review of Biology},
year = {2011},
OPTkey = {•},
volume = {86},
OPTnumber = {•},
pages = {3--34},
OPTmonth = {•},
OPTnote = {•},
OPTannote = {•}
}

@Article{Kendall1948,
author = {Kendall, D.G.},
title = {On the generalized ``birth‐death'' process},
journal = {Annals of Mathematical Statistics},
year = {1948},
OPTkey = {•},
volume = {19},
OPTnumber = {•},
pages = {1--15},
OPTmonth = {•},
OPTnote = {•},
OPTannote = {•}
}

@article{Foote1996,
     jstor_articletype = {research-article},
     title = {On the Probability of Ancestors in the Fossil Record},
     author = {Foote, Mike},
     journal = {Paleobiology},
     jstor_issuetitle = {},
     volume = {22},
     number = {2},
     jstor_formatteddate = {Spring, 1996},
     pages = {141--151},
     url = {http://www.jstor.org/stable/2401114},
     ISSN = {00948373},
     abstract = {Three homogeneous models of species origination and extinction are used to assess the probability that ancestor-descendant pairs are preserved in the fossil record. In the model of cladogenetic budding, a species can persist after it branches and can therefore have multiple direct descendants. In the bifurcation model, a species branches to give rise to two distinct direct descendants, itself terminating in the process. In the model of phyletic transformation, a species gives rise to a single direct descendant without branching, itself terminating in the process. Assuming homogeneous preservation, even under pessimistic assumptions regarding the completeness of the fossil record, the probability of finding fossil ancestor-descendant pairs is not negligible. Even if all species of Phanerozoic marine invertebrates in the paleontologically important taxa had the same probability of preservation, on the order of 1%-10% or more of the known fossil species would be directly ancestral to other known fossil species. However, this is likely to be an underestimate, since the probability of finding ancestor-descendant pairs is enhanced by taxonomic, temporal, and spatial heterogeneities in preservation probability. Moreover, indirect genealogical relationships substantially increase the probability of finding ancestor-descendant pairs. The model of budding, the only one in which an ancestor can persist after a branching event, predicts that half or more of extant species have ancestors that are also extant. Thus, the question of how to recognize ancestor-descendant pairs must be carefully considered.},
     language = {English},
     year = {1996},
     publisher = {Paleontological Society},
     copyright = {Copyright © 1996 Paleontological Society},
    }

@article{Bapst2013,
    author = {Bapst, , David W.},
    journal = {PLoS ONE},
    publisher = {Public Library of Science},
    title = {When Can Clades Be Potentially Resolved with Morphology?},
    year = {2013},
    month = {04},
    volume = {8},
    url = {http://dx.doi.org/10.1371%2Fjournal.pone.0062312},
    pages = {e62312},
    abstract = {<sec><title/><p>Morphology-based phylogenetic analyses are the only option for reconstructing relationships among extinct lineages, but often find support for conflicting hypotheses of relationships. The resulting lack of phylogenetic resolution is generally explained in terms of data quality and methodological issues, such as character selection. A previous suggestion is that sampling ancestral morphotaxa or sampling multiple taxa descended from a long-lived, unchanging lineage can also yield clades which have no opportunity to share synapomorphies. This lack of character information leads to a lack of ‘intrinsic’ resolution, an issue that cannot be solved with additional morphological data. It is unclear how often we should expect clades to be intrinsically resolvable in realistic circumstances, as intrinsic resolution must increase as taxonomic sampling decreases. Using branching simulations, I quantify intrinsic resolution across several models of morphological differentiation and taxonomic sampling. Intrinsically unresolvable clades are found to be relatively frequent in simulations of both extinct and living taxa under realistic sampling scenarios, implying that intrinsic resolution is an issue for morphology-based analyses of phylogeny. Simulations which vary the rates of sampling and differentiation were tested for their agreement to observed distributions of durations from well-sampled fossil records and also having high intrinsic resolution. This combination only occurs in those datasets when differentiation and sampling rates are both unrealistically high relative to branching and extinction rates. Thus, the poor phylogenetic resolution occasionally observed in morphological phylogenetics may result from a lack of intrinsic resolvability within groups.</p></sec>},
    number = {4},
    doi = {10.1371/journal.pone.0062312}
}

@InCollection{HansenHoule2004,
author = {Hansen, Thomas F. and Houle, David},
title = {Evolvability, Stabilizing Selection and the Problem of Stasis},
booktitle = {The Evolutionary Biology of Complex Phenotypes},
OPTcrossref = {•},
OPTkey = {•},
pages = {130--150},
publisher = {Oxford University Press},
year = {2004},
editor = {M Pigliucci and K Preston},
OPTvolume = {•},
OPTnumber = {•},
OPTseries = {•},
OPTtype = {•},
OPTchapter = {•},
OPTaddress = {•},
OPTedition = {•},
OPTmonth = {•},
OPTnote = {•},
OPTannote = {•}
}

@article{WalshBlows2009,
author = {Walsh, Bruce and Blows, Mark W.},
title = {Abundant Genetic Variation + Strong Selection = Multivariate Genetic Constraints: A Geometric View of Adaptation},
journal = {Annual Review of Ecology, Evolution, and Systematics},
volume = {40},
number = {1},
pages = {41--59},
year = {2009},
doi = {10.1146/annurev.ecolsys.110308.120232},

URL = {http://www.annualreviews.org/doi/abs/10.1146/annurev.ecolsys.110308.120232},
eprint = {http://www.annualreviews.org/doi/pdf/10.1146/annurev.ecolsys.110308.120232}
}

@Book{Okasha2006,
author = {Okasha, Samir},
ALTeditor = {•},
title = {Evolution and the Levels of Selection},
publisher = {Oxford University Press},
year = {2006},
OPTkey = {•},
OPTvolume = {•},
OPTnumber = {•},
OPTseries = {•},
OPTaddress = {•},
OPTedition = {•},
OPTmonth = {•},
OPTnote = {•},
OPTannote = {•}
}

@article {Frank2012,
author = {Frank, S. A.},
title = {Natural selection. IV. The {P}rice equation},
journal = {Journal of Evolutionary Biology},
volume = {25},
number = {6},
publisher = {Blackwell Publishing Ltd},
issn = {1420-9101},
url = {http://dx.doi.org/10.1111/j.1420-9101.2012.02498.x},
doi = {10.1111/j.1420-9101.2012.02498.x},
pages = {1002--1019},
keywords = {fundamental theorem, invariance expressions, mathematical models, population genetics},
year = {2012},
}

@article {Price1972,
author = {Price, George R.},
title = {Extension of covariance selection mathematics},
journal = {Annals of Human Genetics},
volume = {35},
number = {4},
publisher = {Blackwell Publishing Ltd},
issn = {1469-1809},
url = {http://dx.doi.org/10.1111/j.1469-1809.1957.tb01874.x},
doi = {10.1111/j.1469-1809.1957.tb01874.x},
pages = {485--490},
year = {1972},
}

@article {RaboskyAdams2012,
author = {Rabosky, Daniel L. and Adams, Dean C.},
title = {Rates of morphological evolution are correlated with species richness in salamanders},
journal = {Evolution},
volume = {66},
number = {6},
publisher = {Blackwell Publishing Inc},
issn = {1558-5646},
url = {http://dx.doi.org/10.1111/j.1558-5646.2011.01557.x},
doi = {10.1111/j.1558-5646.2011.01557.x},
pages = {1807--1818},
keywords = {Adaptive radiation, macroevolution, morphological evolution, phylogenetics, speciation},
year = {2012},
}

@article{Grantham1995,
     jstor_articletype = {research-article},
     title = {Hierarchical Approaches to Macroevolution: Recent Work on Species Selection and the "Effect Hypothesis"},
     author = {Grantham, Todd A.},
     journal = {Annual Review of Ecology and Systematics},
     jstor_issuetitle = {},
     volume = {26},
     number = {},
     jstor_formatteddate = {1995},
     pages = {301--321},
     url = {http://www.jstor.org/stable/2097209},
     ISSN = {00664162},
     abstract = {After briefly introducing the hierarchical perspective, I discuss several theoretical issues concerning the nature of species selection and Vrba's effect hypothesis, and I review recent empirical evidence supporting hierarchical approaches to macroevolution. I argue that Vrba's influential definition of species selection is flawed in two ways. First, species selection does not require emergent traits because higher-level selection acting on aggregate traits can oppose lower-level selection. Second, clades do not play the same role in species selection that populations play in organismic selection. If explanatory and ontological reductionism are distinguished, then even though effect macroevolution does not involve a distinct macroevolutionary process, effect hypothesis explanations can be irreducible. A few well-documented cases of species selection and effect macroevolution suggest the need for a hierarchical expansion of neodarwinism.},
     language = {English},
     year = {1995},
     publisher = {Annual Reviews},
     copyright = {Copyright © 1995 Annual Reviews},
    }

@article{JablonskiHunt2006,
     jstor_articletype = {brief-report},
     title = {Larval Ecology, Geographic Range, and Species Survivorship in {C}retaceous Mollusks: Organismic versus Species-Level Explanations.},
     author = {David Jablonski and Gene Hunt},
     journal = {The American Naturalist},
     jstor_issuetitle = {},
     volume = {168},
     number = {4},
     jstor_formatteddate = {October 2006},
     pages = {556--564},
     url = {http://www.jstor.org/stable/10.1086/507994},
     ISSN = {00030147},
     abstract = {Abstract: The observation that geographic range size in Cretaceous mollusks is correlated with species survivorship and is heritable at the species level has figured repeatedly in discussions of species selection over the past two decades. However, some authors have suggested that the relationship between mode of larval development and geographic range supports the reduction of this example to selection on organismic properties. Our reanalysis of Jablonski's work on heritability at the species level finds that geographic range is significantly heritable (using a randomization test) in both bivalves and gastropods, even within a single larval mode. Further, generalized linear models show that geographic range size is more important than larval mode in predicting extinction probability in both gastropods and bivalves. These results reaffirm the role and heritability of geographic range as a species‐level property that can promote species selection; the model‐based approach applied here may help to operationalize “screening off ” and related approaches to evaluating hierarchical explanations in evolution.},
     language = {English},
     year = {2006},
     publisher = {The University of Chicago Press for The American Society of Naturalists},
     copyright = {Copyright © 2006 The University of Chicago},
    }

@article{Harnik2011,
author = {Harnik, Paul G.},
title = {Direct and indirect effects of biological factors on extinction risk in fossil bivalves},
volume = {108},
number = {33},
pages = {13594--13599},
year = {2011},
doi = {10.1073/pnas.1100572108},
abstract ={Biological factors, such as abundance and body size, may contribute directly to extinction risk and indirectly through their influence on other biological characteristics, such as geographic range size. Paleontological data can be used to explicitly test many of these hypothesized relationships, and general patterns revealed through analysis of the fossil record can help refine predictive models of extinction risk developed for extant species. Here, I use structural equation modeling to tease apart the contributions of three canonical predictors of extinction—abundance, body size, and geographic range size—to the duration of bivalve species in the early Cenozoic marine fossil record of the eastern United States. I find that geographic range size has a strong direct effect on extinction risk and that an apparent direct effect of abundance can be explained entirely by its covariation with geographic range. The influence of geographic range on extinction risk is manifest across three ecologically disparate bivalve clades. Body size also has strong direct effects on extinction risk but operates in opposing directions in different clades, and thus, it seems to be decoupled from extinction risk in bivalves as a whole. Although abundance does not directly predict extinction risk, I reveal weak indirect effects of both abundance and body size through their positive influence on geographic range size. Multivariate models that account for the pervasive covariation between biological factors and extinction are necessary for assessing causality in evolutionary processes and making informed predictions in applied conservation efforts.},
URL = {http://www.pnas.org/content/108/33/13594.abstract},
eprint = {http://www.pnas.org/content/108/33/13594.full.pdf+html},
journal = {Proceedings of the National Academy of Sciences}
}

@article{Harnik2012,
author = {Harnik, Paul G. and Simpson, Carl and Payne, Jonathan L.},
title = {Long-term differences in extinction risk among the seven forms of rarity},
volume = {279},
number = {1749},
pages = {4969--4976},
year = {2012},
doi = {10.1098/rspb.2012.1902},
abstract ={Rarity is widely used to predict the vulnerability of species to extinction. Species can be rare in markedly different ways, but the relative impacts of these different forms of rarity on extinction risk are poorly known and cannot be determined through observations of species that are not yet extinct. The fossil record provides a valuable archive with which we can directly determine which aspects of rarity lead to the greatest risk. Previous palaeontological analyses confirm that rarity is associated with extinction risk, but the relative contributions of different types of rarity to extinction risk remain unknown because their

license: MIT

license_type: permissive

branch_name: refs/heads/master

extension: bib