text:
@article{Agutter2004,
   author = {Agutter, Paul S and Wheatley, Denys N},
   title = {Metabolic scaling: consensus or controversy?},
   journal = {Theoretical Biology and Medical Modelling},
   volume = {1},
   number = {1},
   pages = {13},
   abstract = {The relationship between body mass (M) and standard metabolic rate (B) among living organisms remains controversial, though it is widely accepted that in many cases B is approximately proportional to the three-quarters power of M.},
   DOI = {10.1186/1742-4682-1-13},
   url = {http://www.tbiomed.com/content/1/1/13
http://www.tbiomed.com/content/pdf/1742-4682-1-13.pdf},
   year = {2004},
   type = {Journal Article}
}

@article{Banavar2002,
   author = {Banavar, Jayanth R and Damuth, John and Maritan, Amos and Rinaldo, Andrea},
   title = {Supply-demand balance and metabolic scaling.},
   journal = {Proceedings of the National Academy of Sciences},
   volume = {99},
   number = {16},
   pages = {10506-10509},
   abstract = {It is widely accepted that metabolic rates scale across species approximately as the 3/4 power of mass in most if not all groups of organisms. Metabolic demand per unit mass thus decreases as body mass increases. Metabolic rates reflect both the ability of the organism's transport system to deliver metabolites to the tissues and the rate at which the tissues use them. We show that the ubiquitous 3/4 power law for interspecific metabolic scaling arises from simple, general geometric properties of transportation networks constrained to function in biological organisms. The 3/4 exponent and other observed scaling relationships follow when mass-specific metabolic demands match the changing delivery capacities of the network at different body sizes. Deviation from the 3/4 exponent suggests either inefficiency or compensating physiological mechanisms. Our conclusions are based on general arguments incorporating the minimum of biological detail and should therefore apply to the widest range of organisms.},
   DOI = {10.1073/pnas.162216899},
   url = {http://www.pnas.org/content/99/16/10506.full
http://www.pnas.org/content/99/16/10506.full.pdf},
   year = {2002},
   type = {Journal Article}
}

@article{Banavar2010,
   author = {Banavar, Jayanth R and Moses, Melanie E and Brown, James H and Damuth, John and Rinaldo, Andrea and Sibly, Richard M and Maritan, Amos},
   title = {A general basis for quarter-power scaling in animals.},
   journal = {Proceedings of the National Academy of Sciences of the United States of America},
   volume = {107},
   number = {36},
   pages = {15816-15820},
   abstract = {It has been known for decades that the metabolic rate of animals scales with body mass with an exponent that is almost always <1, >2/3, and often very close to 3/4. The 3/4 exponent emerges naturally from two models of resource distribution networks, radial explosion and hierarchically branched, which incorporate a minimum of specific details. Both models show that the exponent is 2/3 if velocity of flow remains constant, but can attain a maximum value of 3/4 if velocity scales with its maximum exponent, 1/12. Quarter-power scaling can arise even when there is no underlying fractality. The canonical "fourth dimension" in biological scaling relations can result from matching the velocity of flow through the network to the linear dimension of the terminal "service volume" where resources are consumed. These models have broad applicability for the optimal design of biological and engineered systems where energy, materials, or information are distributed from a single source.},
   DOI = {10.1073/pnas.1009974107},
   url = {http://www.pnas.org/content/107/36/15816.full
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2936637/pdf/pnas.201009974.pdf},
   year = {2010},
   type = {Journal Article}
}

@article{Bokma2004,
   author = {Bokma, Folmer},
   title = {Evidence against universl metabolic theory},
   journal = {Functional Ecology},
   volume = {18},
   pages = {184-187},
   year = {2004},
   type = {Journal Article}
}

@article{Capellini2010,
   author = {Capellini, Isabella and Venditti, Chris and Barton, Robert A},
   title = {Phylogeny and metabolic scaling in mammals},
   journal = {Ecology},
   volume = {91},
   number = {9},
   pages = {2783-2793},
   DOI = {10.1890/09-0817.1},
   url = {http://www.esajournals.org/doi/abs/10.1890/09-0817.1
http://www.esajournals.org/doi/pdf/10.1890/09-0817.1},
   year = {2010},
   type = {Journal Article}
}

@article{ClarkeJohnston1999,
   author = {Clarke, A and Johnston, N M},
   title = {Scaling of metabolic rate with body mass and temperature in teleost fish},
   journal = {Journal of Animal Ecology},
   volume = {68},
   number = {5},
   pages = {893-905},
   DOI = {10.1046/j.1365-2656.1999.00337.x},
   url = {http://onlinelibrary.wiley.com/doi/10.1046/j.1365-2656.1999.00337.x/full
http://onlinelibrary.wiley.com/store/10.1046/j.1365-2656.1999.00337.x/asset/j.1365-2656.1999.00337.x.pdf?v=1&t=i4k7i0us&s=d95d66d2452ca47e052fca08ff9c2077834952ff},
   year = {1999},
   type = {Journal Article}
}

@article{DawsonWolfers1978,
   author = {DAWSON, T J and WOLFERS, J M},
   title = {Metabolism, Thermoregulation and Torpor in Shrew Sized Marsupials of Genus Planigale},
   journal = {Comparative Biochemistry and Physiology a-Physiology},
   volume = {59},
   number = {3},
   pages = {305-309},
   DOI = {10.1016/0300-9629(78)90167-6},
   url = {http://linkinghub.elsevier.com/retrieve/pii/0300962978901676},
   year = {1978},
   type = {Journal Article}
}

@article{DeLong2010,
   author = {DeLong, J and Okie, J and Moses, M},
   title = {Shifts in metabolic scaling, production, and efficiency across major evolutionary transitions of life},
   journal = {Human population reduction is not a quick fix for environmental problems},
   url = {http://www.pnas.org/content/early/2010/06/25/1007783107.full.pdf},
   year = {2010},
   type = {Journal Article}
}

@article{Dodds2001,
   author = {Dodds, P S and Rothman, D H and Weitz, J S},
   title = {Re-examination of the “3/4-law” of Metabolism},
   journal = {Journal of Theoretical Biology},
   volume = {209},
   number = {1},
   pages = {9-27},
   DOI = {10.1006/jtbi.2000.2238},
   year = {2001},
   type = {Journal Article}
}

@article{FarrellGray2005,
   author = {Farrell-Gray, C C and Gotelli, N J},
   title = {Allometric exponents support a 3/4-power scaling law},
   journal = {Ecology},
   volume = {86},
   number = {8},
   pages = {2083-2087},
   DOI = {10.1890/04-1618},
   url = {http://www.esajournals.org/doi/abs/10.1890/04-1618
http://www.esajournals.org/doi/pdf/10.1890/04-1618},
   year = {2005},
   type = {Journal Article}
}

@article{Glazier2010,
   author = {Glazier, DS},
   title = {A unifying explanation for diverse metabolic scaling in animals and plants},
   journal = {Biological Reviews},
   abstract = {The scaling of metabolic rate with body mass has long been a controversial topic. Some workers have claimed that the slope of log-log metabolic scaling relationships typically obeys a universal 3/4-power law resulting from the geometry of resource-transport networks. Others have ...},
   url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1469-185X.2009.00095.x/full},
   year = {2010},
   type = {Journal Article}
}

@article{Glazier2014,
   author = {Glazier, Douglas},
   title = {Metabolic Scaling in Complex Living Systems},
   journal = {Systems},
   volume = {2},
   number = {4},
   pages = {451-540},
   abstract = {In this review I show that four major kinds of theoretical approaches have been used to explain the scaling of metabolic rate in cells, organisms and groups of organisms in relation to system size. They include models focusing on surface-area related fluxes of resources and wastes (including heat), internal resource transport, system composition, and various processes affecting resource demand, all of which have been discussed extensively for nearly a century or more. I argue that, although each of these theoretical approaches has been applied to multiple levels of biological organization, none of them alone can fully explain the rich diversity of metabolic scaling relationships, including scaling exponents (log-log slopes) that vary from ~0 to &gt;1. Furthermore, I demonstrate how a synthetic theory of metabolic scaling can be constructed by including the context-dependent action of each of the above modal effects. This “contextual multimodal theory” (CMT) posits that various modulating factors (including metabolic level, surface permeability, body shape, modes of thermoregulation and resource-transport, and other internal and external influences) affect the mechanistic expression of each theoretical module. By involving the contingent operation of several mechanisms, the “meta-mechanistic” CMT differs from most metabolic scaling theories that are deterministically mechanistic. The CMT embraces a systems view of life, and as such recognizes the open, dynamic nature and complex hierarchical and interactive organization of biological systems, and the importance of multiple (upward, downward and reciprocal) causation, biological regulation of resource supply and demand and their interaction, and contingent internal (system) and external (environmental) influences on metabolic scaling, all of which are discussed. I hope that my heuristic attempt at building a unifying theory of metabolic scaling will not only stimulate further testing of all of the various subtheories composing it, but also foster an appreciation that many current models are, at least in part, complementary or even synergistic, rather than antagonistic. Further exploration about how the scaling of the rates of metabolism   and other biological processes are interrelated should also provide the groundwork for formulating a general metabolic theory of biology.},
   DOI = {10.3390/systems2040451},
   url = {http://www.mdpi.com/2079-8954/2/4/451/htm
http://www.mdpi.com/2079-8954/2/4/451/pdf},
   year = {2014},
   type = {Journal Article}
}

@article{Glazier2005,
   author = {Glazier, Douglas S},
   title = {Beyond the '3/4-power' law: variation in the intra- and interspecific scaling of metabolic rate in animals},
   journal = {Biological Reviews},
   volume = {80},
   number = {4},
   pages = {611-662},
   DOI = {10.1017/S1464793105006834},
   url = {http://doi.wiley.com/10.1017/S1464793105006834
http://journals.cambridge.org/download.php?file=%2F6284_5029B83DA0900A52561A51B3D665ADB2_journals__BRE_BRE80_04_S1464793105006834a.pdf&cover=Y&code=1f403b56157bac75a8274c4fdfabca59},
   year = {2005},
   type = {Journal Article}
}

@article{Glazier2014,
   author = {Glazier, D S},
   title = {Is metabolic rate a universal 'pacemaker'for biological processes?},
   journal = {Biological Reviews},
   abstract = {... Recently, some investigators have re-emphasized the importance of energy metabolism in understanding ecological ... factor e −E/kT , where k is Boltzmann's constant and T is temperature in ... in Arrhenius plots also often approximates −0.65 eV for both metabolic  rate and other ... },
   url = {http://onlinelibrary.wiley.com/doi/10.1111/brv.12115/full},
   year = {2014},
   type = {Journal Article}
}

@article{HayssenLacy1985,
   author = {Hayssen, V and Lacy, R C},
   title = {Basal Metabolic Rates in Mammals - Taxonomic Differences in the Allometry of Bmr and Body-Mass},
   journal = {Comparative Biochemistry and Physiology a-Physiology},
   volume = {81},
   number = {4},
   pages = {741-754},
   DOI = {10.1016/0300-9629(85)90904-1},
   url = {http://linkinghub.elsevier.com/retrieve/pii/0300962985909041},
   year = {1985},
   type = {Journal Article}
}

@article{Hudson2013,
   author = {Hudson, Lawrence N and Isaac, Nick J B and Reuman, Daniel C},
   title = {The relationship between body mass and field metabolic rate among individual birds and mammals},
   journal = {Journal of Animal Ecology},
   pages = {n/a-n/a},
   DOI = {10.1111/1365-2656.12086},
   url = {http://doi.wiley.com/10.1111/1365-2656.12086
http://onlinelibrary.wiley.com/store/10.1111/1365-2656.12086/asset/jane12086.pdf?v=1&t=i4k7ifg9&s=7139b2af423c22a8cd3a908a54637bc54dc5e38f},
   year = {2013},
   type = {Journal Article}
}

@article{IsaacCarbone2010,
   author = {Isaac, NJB and Carbone, C},
   title = {Why are metabolic scaling exponents so controversial? Quantifying variance and testing hypotheses},
   journal = {Ecology Letters},
   volume = {13},
   number = {6},
   pages = {728-735},
   url = {http://onlinelibrary.wiley.com/store/10.1111/j.1461-0248.2010.01461.x/asset/j.1461-0248.2010.01461.x.pdf?v=1&t=i4k7ip01&s=0da5ea4804f830f0c11f9720be227a3a1f6e799b},
   year = {2010},
   type = {Journal Article}
}

@article{Killen2010,
   author = {Killen, SS and Atkinson, D and Glazier, DS},
   title = {The intraspecific scaling of metabolic rate with body mass in fishes depends on lifestyle and temperature},
   journal = {Ecology Letters},
   volume = {13},
   number = {2},
   pages = {184-193},
   url = {http://onlinelibrary.wiley.com/store/10.1111/j.1461-0248.2009.01415.x/asset/j.1461-0248.2009.01415.x.pdf?v=1&t=i4k7itrh&s=7d2f23766e48abc27431eb6030d3696975a723a0},
   year = {2010},
   type = {Journal Article}
}

@article{Kolokotrones2010,
   author = {Kolokotrones, Tom and Savage, V M and Deeds, Eric J and Fontana, Walter},
   title = {Curvature in metabolic scaling},
   journal = {Nature},
   volume = {464},
   number = {7289},
   pages = {753-756},
   DOI = {10.1038/nature08920},
   url = {http://www.nature.com/doifinder/10.1038/nature08920
http://www.nature.com/nature/journal/v464/n7289/pdf/nature08920.pdf},
   year = {2010},
   type = {Journal Article}
}

@article{Lovegrove2000,
   author = {Lovegrove, BG},
   title = {The Zoogeography of Mammalian Basal Metabolic Rate.},
   journal = {The American Naturalist},
   volume = {156},
   number = {2},
   pages = {201-219},
   abstract = {Zoogeographical effects on the basal metabolic rate (BMR) of 487 mammal species were analyzed using conventional and phylogenetically independent ANCOVA. Minimal BMR variance occurred at a "constrained body mass" of 358 g, whereas maximum variance occurred at the smallest and largest body masses. Significant differences in BMR were identified for similar-sized mammals from the six terrestrial zoogeographical zones (Afrotropical, Australasian, Indomalayan, Nearctic, Neotropical, and Palearctic). Nearctic and Palearctic mammals had higher basal rates than their Afrotropical, Australasian, Indomalayan, and Neotropical counterparts. Desert mammals had lower basal rates than mesic mammals. The patterns were interpreted with a conceptual model describing geographical BMR variance in terms of the influence of latitudinal and zonal climate variability. Low and high basal rates were explained in unpredictable and predictable environments, respectively, especially in small mammals. The BMR of large mammals may be influenced in addition by mobility and predation constraints. Highly mobile mammals tend to have high BMRs that may somehow facilitate fast running speeds, whereas less mobile mammals are generally dietary specialists and are often armored. The model thus integrates physiological and ecological criteria and makes predictions concerning body size and life-history evolution, island effects, and locomotor energetics.},
   url = {http://www.jstor.org/stable/pdfplus/10.1086/303383.pdf?acceptTC=true},
   year = {2000},
   type = {Journal Article}
}

@article{Maino2013,
   author = {Maino, James L and Kearney, Michael R and Nisbet, Roger M and Kooijman, Sebastiaan A L M},
   title = {Reconciling theories for metabolic scaling},
   journal = {Journal of Animal Ecology},
   pages = {n/a-n/a},
   DOI = {10.1111/1365-2656.12085},
   url = {http://doi.wiley.com/10.1111/1365-2656.12085
http://onlinelibrary.wiley.com/store/10.1111/1365-2656.12085/asset/jane12085.pdf?v=1&t=i4k7iyrh&s=0549de736f8cfd8870d8af40418ba35f475d56f6},
   year = {2013},
   type = {Journal Article}
}

@article{Makarieva2008,
   author = {Makarieva, Anastassia M and Gorshkov, Victor G and Li, Bai-Lian and Chown, Steven L and Reich, Peter B and Gavrilov, Valery M},
   title = {Mean mass-specific metabolic rates are strikingly similar across life's major domains: Evidence for life's metabolic optimum},
   journal = {Proceedings of the National Academy of Sciences},
   volume = {105},
   number = {44},
   pages = {16994-16999},
   DOI = {10.1073/pnas.0802148105},
   url = {http://www.pnas.org/cgi/doi/10.1073/pnas.0802148105
http://www.pnas.org/content/105/44/16994.full.pdf},
   year = {2008},
   type = {Journal Article}
}

@article{McKechnie2006,
   author = {McKechnie, Andrew E and Freckleton, Robert P and Jetz, Walter},
   title = {Phenotypic plasticity in the scaling of avian basal metabolic rate},
   journal = {Proceedings of the Royal Society of London B: Biological Sciences},
   volume = {273},
   number = {1589},
   pages = {931-937},
   abstract = {Many birds exhibit short-term, reversible adjustments in basal metabolic rate (BMR), but the overall contribution of phenotypic plasticity to avian metabolic diversity remains unclear. The available BMR data include estimates from birds living in natural environments and captive-raised birds in more homogenous, artificial environments. All previous analyses of interspecific variation in BMR have pooled these data. We hypothesized that phenotypic plasticity is an important contributor to interspecific variation in avian BMR, and that captive-raised populations exhibit general differences in BMR compared to wild-caught populations. We tested this hypothesis by fitting general linear models to BMR data for 231 bird species, using the generalized least-squares approach to correct for phylogenetic relatedness when necessary. The scaling exponent relating BMR to body mass in captive-raised birds (0.670) was significantly shallower than in wild-caught birds (0.744). The differences in metabolic scaling between captive-raised and wild-caught birds persisted when migratory tendency and habitat aridity were controlled for. Our results reveal that phenotypic plasticity is a major contributor to avian interspecific metabolic variation. The finding that metabolic scaling in birds is partly determined by environmental factors provides further support for models that predict variation in scaling exponents, such as the allometric cascade model.},
   DOI = {10.1098/rspb.2005.3415},
   url = {http://rspb.royalsocietypublishing.org/cgi/doi/10.1098/rspb.2005.3415
http://rspb.royalsocietypublishing.org/content/royprsb/273/1589/931.full.pdf},
   year = {2006},
   type = {Journal Article}
}

@article{McKechnieWolf2004,
   author = {McKechnie, A E and Wolf, B O},
   title = {The allometry of avian basal metabolic rate: good predictions need good data},
   journal = {Physiological and Biochemical Zoology},
   volume = {77},
   number = {3},
   pages = {502-521},
   DOI = {10.1086/383511},
   url = {http://www.jstor.org/stable/10.1086/383511
http://www.jstor.org/stable/pdfplus/10.1086/383511.pdf},
   year = {2004},
   type = {Journal Article}
}

@article{McNab1986,
   author = {Mcnab, Brian K},
   title = {The Influence of Food Habits on the Energetics of Eutherian Mammals},
   journal = {Ecological Monographs},
   volume = {56},
   number = {1},
   pages = {1},
   DOI = {10.2307/2937268},
   url = {http://www.jstor.org/stable/2937268?origin=crossref},
   year = {1986},
   type = {Journal Article}
}

@article{McNab1988,
   author = {Mcnab, Brian K},
   title = {Complications Inherent in Scaling the Basal Rate of Metabolism in Mammals},
   journal = {The Quarterly Review of Biology},
   volume = {63},
   number = {1},
   pages = {25-54},
   abstract = {The scaling of the basal rate of metabolism in mammals is reexamined. Both the power and level of the scaling function are sensitive to various factors that interact with body mass and rate of metabolism, including the precision of temperature regulation, food habits, and activity level. This sensitivity implies that the rate of metabolism is a highly plastic character in the course of evolution. Consequently, the singular effect of mass on the rate of metabolism is most effectively analyzed in ecologically and physiologically uniform sets of species, rather than in taxonomically defined groups, which often are ecologically and physiologically diverse. Otherwise, all fitted curves for mammals integrate a variety of competing factors, thereby reflecting the species used and denying unique analytic significance to the power in scaling relations. Kleiber's eutherian curve may represent a relatively uniform set of data because all the species included were domesticated and because selection for high rates of production (and high rates of metabolism) occurred in the process of domestication. In the analysis of scaling relationships, the standard error of estimate (Sy· x) is a more valuable measure of the residual variation than is (1.0 - r<sup>2</sup>) because r<sup>2</sup> is a non-linear measure of the conformation of data to the relation and because Sy· x, unlike r<sup>2</sup>, is independent of the units used in the scaling relationship. At present the best estimate indicates that total rate of metabolism scales proportionally to approximately m<sup>0</sup>.60 at small masses (< 300 g), as long as small species do not enter torpor, and scales proportionally to approximately m<sup>0</sup>.75 a large masses (⩾ 300 g). Physiolgocal properties other than metabolism are potentially sensitive to secondary factors, so their scaling functions also would be most clearly defined for physiologically uniform groups of species. This view suggests that insight into the significance of scaling relations can be obtained by examining the residual variation around a scaling function as well as by examining conformation to the function.},
   DOI = {10.2307/2827977},
   url = {http://www.jstor.org/stable/2827977},
   year = {1988},
   type = {Journal Article}
}

@article{McNab2000,
   author = {Mcnab, Brian K},
   title = {Metabolic scaling: Energy constraints on carnivore diet},
   journal = {Nature News},
   volume = {407},
   number = {6804},
   pages = {584-584},
   DOI = {10.1038/35036695},
   url = {http://www.nature.com/doifinder/10.1038/35036695
http://www.nature.com/nature/journal/v407/n6804/pdf/407584a0.pdf},
   year = {2000},
   type = {Journal Article}
}

@article{Nagy1987,
   author = {Nagy, Kenneth A},
   title = {Field Metabolic Rate and Food Requirement Scaling in Mammals and Birds},
   journal = {Ecological Monographs},
   volume = {57},
   number = {2},
   pages = {111},
   DOI = {10.2307/1942620},
   url = {http://www.jstor.org/stable/1942620?origin=crossref},
   year = {1987},
   type = {Journal Article}
}

@article{Savage2004,
   author = {Savage, V M and Gillooly, James F and Woodruff, William H and West, Geoggrey B and Allen, Andrew P and Enquist, Brian J and Brown, James H},
   title = {The predominance of quarter-power scaling in biology},
   journal = {Functional Ecology},
   volume = {18},
   pages = {257-282},
   year = {2004},
   type = {Journal Article}
}

@article{Sieg2009,
   author = {Sieg, Annette E and O’Connor, Michael P and McNair, James N and Grant, Bruce W and Agosta, Salvatore J and Dunham, Arthur E},
   title = {Mammalian Metabolic Allometry: Do Intraspecific Variation, Phylogeny, and Regression Models Matter?},
   journal = {The American Naturalist},
   volume = {174},
   number = {5},
   pages = {720-733},
   DOI = {10.1086/606023},
   url = {http://www.jstor.org/stable/10.1086/606023
http://www.jstor.org/stable/pdfplus/10.1086/606023.pdf},
   year = {2009},
   type = {Journal Article}
}

@article{White2006,
   author = {White, C R and Phillips, N F and Seymour, R S},
   title = {The scaling and temperature dependence of vertebrate metabolism},
   journal = {Biology Letters},
   volume = {2},
   number = {1},
   pages = {125-127},
   DOI = {10.1098/rsbl.2005.0378},
   url = {http://rsbl.royalsocietypublishing.org/cgi/doi/10.1098/rsbl.2005.0378
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1617203/pdf/rsbl20050378.pdf},
   year = {2006},
   type = {Journal Article}
}

@article{McClain2012,
   author = {McClain, C.R. and Allen, A.P. and Tittensor, D.P. and Rex, M A},
   title = {The energetics of life on the deep seafloor},
   journal = {Proceedings of the National Academy of Science, U.S.A.},
   volume = {109},
   pages = {5366–15371},
   year = {2012},
   type = {Journal Article}
}

@book{Peters1983,
   author = {Peters, R.H.},
   title = {The ecological implications of body size},
   publisher = {Cambridge University Press},
   address = {Cambridge, United Kingdom},
   year = {1983},
   type = {Book}
}

@book{Calder1984,
   author = {Calder, W.A.},
   title = {Size, Function, and Life History},
   publisher = {Dover Publications, Inc.},
   address = {Mineola, New York},
   year = {1984},
   type = {Book}
}

@article{McClain2014,
   author = {McClain, C.R. and Filler, R. and Auld, J.R.},
   title = {Does energy availaiblity predict gastropod reproductive strategies?},
   journal = {Proceeding of the Royal Society B: Biological Sciences},
   volume = {281},
   pages = {20140400},
   year = {2014},
   type = {Journal Article}
}

@article{Finnegan2011,
   author = {Finnegan, S. and McClain, C.R. and Kosnik, M. and Payne, J.L.},
   title = {Escargot through time: an energetic compariosn of marine gastropods assemblages beofore and after the Mesozoic Marine Revolution},
   journal = {Paleobiology},
   volume = {37},
   pages = {252-269},
   year = {2011},
   type = {Journal Article}
}

@article{Payne2014,
   author = {Payne, J.L. and Heim, N.A. and Knope, M.L. and mcClain, C.R.},
   title = {Metabolic dominance of bivalves predates brachiopod diversity decline by more than 150 million years},
   journal = {Proceeding of the Royal Society B: Biological Sciences},
   volume = {281},
   pages = {20133122},
   year = {2014},
   type = {Journal Article}
}

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@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 = {•},
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}

@article{Alfaro2009,
  title={Does evolutionary innovation in pharyngeal jaws lead to rapid lineage diversification in labrid fishes?},
  author={Alfaro, Michael E and Brock, Chad D and Banbury, Barbara L and Wainwright, Peter C},
  journal={BMC evolutionary biology},
  volume={9},
  number={1},
  pages={255},
  year={2009},
  publisher={BioMed Central Ltd}
}

@article{Frederich2014,
  title={Trait decoupling promotes evolutionary diversification of the trophic and acoustic system of damselfishes},
  author={Fr{\'e}d{\'e}rich, Bruno and Olivier, Damien and Litsios, Glenn and Alfaro, Michael E and Parmentier, Eric},
  journal={Proceedings of the Royal Society B: Biological Sciences},
  volume={281},
  number={1789},
  pages={20141047},
  year={2014},
  publisher={The Royal Society}
}

@article{Near2012,
  title={Ancient climate change, antifreeze, and the evolutionary diversification of Antarctic fishes},
  author={Near, Thomas J and Dornburg, Alex and Kuhn, Kristen L and Eastman, Joseph T and Pennington, Jillian N and Patarnello, Tomaso and Zane, Lorenzo and Fern{\'a}ndez, Daniel A and Jones, Christopher D},
  journal={Proceedings of the National Academy of Sciences},
  volume={109},
  number={9},
  pages={3434--3439},
  year={2012},
  publisher={National Acad Sciences}
}

@article{SandersonDonoghue1996,
  title={Reconstructing shifts in diversification rates on phylogenetic trees},
  author={Sanderson, Michael J and Donoghue, Michael J},
  journal={Trends in Ecology \& Evolution},
  volume={11},
  number={1},
  pages={15--20},
  year={1996},
  publisher={Elsevier}
}

@article{Lande1979,
  title={Quantitative genetic analysis of multivariate evolution, applied to brain: body size allometry},
  author={Lande, Russell},
  journal={Evolution},
  pages={402--416},
  year={1979},
  publisher={JSTOR}
}

@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{Gillooly2001,
  title={Effects of size and temperature on metabolic rate},
  author={Gillooly, James F and Brown, James H and West, Geoffrey B and Savage, Van M and Charnov, Eric L},
  journal={Science},
  volume={293},
  number={5538},
  pages={2248--2251},
  year={2001},
  publisher={American Association for the Advancement of Science}
}

@article{Payne2013,
  title={A SHIFT IN THE LONG-TERM MODE OF FORAMINIFERAN SIZE EVOLUTION CAUSED BY THE END-PERMIAN MASS EXTINCTION},
  author={Payne, Jonathan L and Jost, Adam B and Wang, Steve C and Skotheim, Jan M},
  journal={Evolution},
  volume={67},
  number={3},
  pages={816--827},
  year={2013},
  publisher={Wiley Online Library}
}

@article{Gavrilets2000,
  title={Rapid evolution of reproductive barriers driven by sexual conflict},
  author={Gavrilets, Sergey},
  journal={Nature},
  volume={403},
  number={6772},
  pages={886--889},
  year={2000},
  publisher={Nature Publishing Group}
}

@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}}

@article{Roff2000,
  title={The evolution of the G matrix: selection or drift?},
  author={Roff, Derek},
  journal={Heredity},
  volume={84},
  number={2},
  pages={135--142},
  year={2000},
  publisher={Nature Publishing Group}
}

@article{BeginRoff2004,
  title={From micro-to macroevolution through quantitative genetic variation: positive evidence from field crickets},
  author={B{\'e}gin, Mattieu and Roff, Derek A},
  journal={Evolution},
  volume={58},
  number={10},
  pages={2287--2304},
  year={2004},
  publisher={Wiley Online Library}
}

@article{Houle1992,
  title={Comparing evolvability and variability of quantitative traits.},
  author={Houle, David},
  journal={Genetics},
  volume={130},
  number={1},
  pages={195--204},
  year={1992},
  publisher={Genetics Soc America}
}

@article{MerilaBjorklund1999,
  title={Population divergence and morphometric integration in the green-finch (Carduelis chloris) -- evolution against the trajectory of least resistance?},
  author={Meril{\"a}, J and Bj{\"o}rklund, M},
  year={1999},
  publisher={Wiley Online Library}
}

@article{MarroigCheverud2004,
  title={Did natural selection or genetic drift produce the cranial diversification of neotropical monkeys?},
  author={Marroig, Gabriel and Cheverud, James M},
  journal={The American Naturalist},
  volume={163},
  number={3},
  pages={417--428},
  year={2004},
  publisher={JSTOR}
}

@article{AckermannCheverud2002,
  title={Discerning evolutionary processes in patterns of tamarin (genus Saguinus) craniofacial variation},
  author={Rogers Ackermann, Rebecca and Cheverud, James M},
  journal={American Journal of Physical Anthropology},
  volume={117},
  number={3},
  pages={260--271},
  year={2002},
  publisher={Wiley Online Library}
}

@article{Felsenstein1981,
  title={Skepticism towards Santa Rosalia, or why are there so few kinds of animals?},
  author={Felsenstein, Joseph},
  journal={Evolution},
  pages={124--138},
  year={1981},
  publisher={JSTOR}
}

@article{Futuyma1995,
  title={Genetic constraints on macroevolution: the evolution of host affiliation in the leaf beetle genus Ophraella},
  author={Futuyma, Douglas J and Keese, Mark C and Funk, Daniel J},
  journal={Evolution},
  pages={797--809},
  year={1995},
  publisher={JSTOR}
}

@article{NosilSandoval2008,
  title={Ecological niche dimensionality and the evolutionary diversification of stick insects},
  author={Nosil, Patrik and Sandoval, Cristina P},
  journal={PLoS One},
  volume={3},
  number={4},
  pages={e1907},
  year={2008},
  publisher={Public Library of Science}
}

@article{WellbornLangerhans2014,
  title={Ecological opportunity and the adaptive diversification of lineages},
  author={Wellborn, Gary A and Langerhans, R Brian},
  journal={Ecology and Evolution},
  year={2014},
  publisher={Wiley Online Library}
}

@article{Pennell2014,
  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},
  volume={29},
  number={1},
  pages={23--32},
  year={2014},
  publisher={Elsevier}
}

@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{Maddison2007,
author = {Maddison, Wayne P. and Midford, Peter E. and Otto, Sarah P.},
title = {Estimating a Binary Character's Effect on Speciation and Extinction},
volume = {56},
number = {5},
pages = {701-710},
year = {2007},
doi = {10.1080/10635150701607033},
abstract ={Determining whether speciation and extinction rates depend on the state of a particular character has been of long-standing interest to evolutionary biologists. To assess the effect of a character on diversification rates using likelihood methods requires that we be able to calculate the probability that a group of extant species would have evolved as observed, given a particular model of the character's effect. Here we describe how to calculate this probability for a phylogenetic tree and a two-state (binary) character under a simple model of evolution (the ‚ÄúBiSSE‚Äù model, binary-state speciation and extinction). The model involves six parameters, specifying two speciation rates (rate when the lineage is in state 0; rate when in state 1), two extinction rates (when in state 0; when in state 1), and two rates of character state change (from 0 to 1, and from 1 to 0). Using these probability calculations, we can do maximum likelihood inference to estimate the model's parameters and perform hypothesis tests (e.g., is the rate of speciation elevated for one character state over the other?). We demonstrate the application of the method using simulated data with known parameter values.},
URL = {http://sysbio.oxfordjournals.org/content/56/5/701.abstract},
eprint = {http://sysbio.oxfordjournals.org/content/56/5/701.full.pdf+html},
journal = {Systematic Biology}
}

@article{MagnusonFord2012,
     jstor_articletype = {research-article},
     title = {Linking the Investigations of Character Evolution and Species Diversification.},
     author = {Magnuson-Ford, Karen and Otto, Sarah P.},
     journal = {The American Naturalist},
     jstor_issuetitle = {},
     volume = {180},
     number = {2},
     jstor_formatteddate = {August 2012},
     pages = {225-245},
     url = {http://www.jstor.org/stable/10.1086/666649},
     ISSN = {00030147},
     abstract = {Abstract Variation in diversification rates is often studied by investigating traits related to species’ ecology and life history. Often, however, it is unknown whether these traits evolve gradually or in punctuated bursts during speciation. Using phylogenetic data and species’ present-day trait information, we present a novel approach to assessing the mode of character change while accounting for trait-dependent speciation and extinction. Our model, “Binary-State Speciation and Extinction–node enhanced state shift” (BiSSE-ness), estimates both the rate of change occurring along lineages and the probability of change occurring during speciation, as well as independent speciation and extinction rates for each character state. Using simulations, we found that BiSSE-ness is able to distinguish along-lineage and speciational change and accurately estimate the parameters associated with character change and diversification rates. We applied BiSSE-ness to an empirical primate data set and found evidence for along-lineage changes in primate mating systems and social behaviors, whereas shifts in habitat were associated with speciation. In cases where trait changes may be linked to the speciation process itself (e.g., niche-related traits), BiSSE-ness provides a suitable framework with which to simultaneously address questions regarding species diversification and character change.},
     language = {English},
     year = {2012},
     publisher = {The University of Chicago Press for The American Society of Naturalists},
     copyright = {Copyright © 2012 The University of Chicago},
    }

@article{RaboskyMcCune2010,
title = "Reinventing species selection with molecular phylogenies",
journal = "Trends in Ecology and 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 {Goldberg2012,
author = {Goldberg, Emma E. and Igi\'{c}, Boris},
title = {Tempo and Mode in Plant Breeding System Evolution},
journal = {Evolution},
volume = {66},
number = {12},
publisher = {Blackwell Publishing Inc},
issn = {1558-5646},
url = {http://dx.doi.org/10.1111/j.1558-5646.2012.01730.x},
doi = {10.1111/j.1558-5646.2012.01730.x},
pages = {3701--3709},
keywords = {Comparative methods, Dollo’s law, macroevolution, self-incompatibility, Solanaceae},
year = {2012},
}

@Book{Gould2002,
author = {Gould, Stephen Jay},
ALTeditor = {•},
title = {The Structure of Evolutionary Theory},
publisher = {Harvard University Press},
year = {2002},
OPTkey = {•},
OPTvolume = {•},
OPTnumber = {•},
OPTseries = {•},
OPTaddress = {•},
OPTedition = {•},
OPTmonth = {•},
OPTnote = {•},
OPTannote = {•}
}

@article{Goldberg2010,
author = {Goldberg, Emma E. and Kohn, Joshua R. and Lande, Russell and Robertson, Kelly A. and Smith, Stephen A. and Igi\'{c}, Boris},
title = {Species Selection Maintains Self-Incompatibility},
volume = {330},
number = {6003},
pages = {493-495},
year = {2010},
doi = {10.1126/science.1194513},
abstract ={Identifying traits that affect rates of speciation and extinction and, hence, explain differences in species diversity among clades is a major goal of evolutionary biology. Detecting such traits is especially difficult when they undergo frequent transitions between states. Self-incompatibility, the ability of hermaphrodites to enforce outcrossing, is frequently lost in flowering plants, enabling self-fertilization. We show, however, that in the nightshade plant family (Solanaceae), species with functional self-incompatibility diversify at a significantly higher rate than those without it. The apparent short-term advantages of potentially self-fertilizing individuals are therefore offset by strong species selection, which favors obligate outcrossing.},
URL = {http://www.sciencemag.org/content/330/6003/493.abstract},
eprint = {http://www.sciencemag.org/content/330/6003/493.full.pdf},
journal = {Science}
}

@article {Futuyma2010,
author = {Futuyma, Douglas J.},
title = {Evolutionary Constraint and Ecological Consequences},
journal = {Evolution},
volume = {64},
number = {7},
publisher = {Blackwell Publishing Inc},
issn = {1558-5646},
url = {http://dx.doi.org/10.1111/j.1558-5646.2010.00960.x},
doi = {10.1111/j.1558-5646.2010.00960.x},
pages = {1865--1884},
keywords = {Community ecology, ephemeral divergence, evolutionary constraint, genetic variation, genostasis, limits to adaptation, phylogenetic conservatism, stasis},
year = {2010},
}

@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.},
     language = {English},
     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},
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/early/2013/01/31/1208302110.abstract},
eprint = {http://www.pnas.org/content/early/2013/01/31/1208302110.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 Bayesian 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{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},
year = {2012},
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/early/2012/12/02/sysbio.sys086.abstract},
eprint = {http://sysbio.oxfordjournals.org/content/early/2012/12/02/sysbio.sys086.full.pdf+html},
journal = {Systematic Biology}
}

@article {Simpson2013,
author = {Simpson, Carl},
title = {Species Selection and the Macroevolution of Coral Coloniality and Photosymbiosis},
journal = {Evolution},
issn = {1558-5646},
url = {http://dx.doi.org/10.1111/evo.12083},
doi = {10.1111/evo.12083},
pages = {},
keywords = {Multilevel selection, Diversification, Paleobiology, Multivariate selection, 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 {Hunt2008,
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{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{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{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{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},
    }

@Book{Gould2002,
author = {Gould, Stephen Jay},
ALTeditor = {•},
title = {The Structure of Evolutionary Theory},
publisher = {Harvard University Press},
year = {2002},
OPTkey = {•},
OPTvolume = {•},
OPTnumber = {•},
OPTseries = {•},
OPTaddress = {•},
OPTedition = {•},
OPTmonth = {•},
OPTnote = {•},
OPTannote = {•}
}

@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-Darwinian 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{Xie2011,
  title={Improving marginal likelihood estimation for {B}ayesian phylogenetic model selection},
  author={Xie, Wangang and Lewis, Paul O and Fan, Yu and Kuo, Lynn and Chen, Ming-Hui},
  journal={Systematic Biology},
  volume={60},
  number={2},
  pages={150--160},
  year={2011},
  publisher={Oxford University Press}
}

@article{Mousseau1987,
  title={Natural selection and the heritability of fitness components},
  author={Mousseau, Timothy A and Roff, Derek A and others},
  journal={Heredity},
  volume={59},
  number={Pt 2},
  pages={181--197},
  year={1987}
}

@Article{Harmon2008,
    title = {GEIGER: investigating evolutionary radiations},
    author = {LJ Harmon and JT Weir and CD Brock and RE Glor and W
      Challenger},
    journal = {Bioinformatics},
    year = {2008},
    volume = {24},
    pages = {129-131},
}

@article{Green1995,
  title={Reversible jump {M}arkov {C}hain {M}onte {C}arlo computation and {B}ayesian model determination},
  author={Green, Peter J},
  journal={Biometrika},
  volume={82},
  number={4},
  pages={711--732},
  year={1995},
  publisher={Biometrika Trust}
}

@article{KassRaftery1995,
  title={Bayes factors},
  author={Kass, Robert E and Raftery, Adrian E},
  journal={Journal of the american statistical association},
  volume={90},
  number={430},
  pages={773--795},
  year={1995},
  publisher={Taylor \& Francis Group}
}

@article{Kass1993,
  title={Bayes factors in practice},
  author={Kass, Robert E},
  journal={The Statistician},
  pages={551--560},
  year={1993},
  publisher={JSTOR}
}

@article{HoAne2013,
  title={Asymptotic theory with hierarchical autocorrelation: {O}rnstein--{U}hlenbeck tree models},
  author={Ho, Lam Si Tung and An{\'e}, C{\'e}cile},
  journal={The Annals of Statistics},
  volume={41},
  number={2},
  pages={957--981},
  year={2013},
  publisher={Institute of Mathematical Statistics}
}

@article{Jaffe2011,
  title={The evolution of island gigantism and body size variation in tortoises and turtles},
  author={Jaffe, Alexander L and Slater, Graham J and Alfaro, Michael E},
  journal={Biology letters},
  volume={7},
  number={4},
  pages={558--561},
  year={2011},
  publisher={The Royal Society}
}

@article{Fan2011,
  title={Choosing among partition models in {B}ayesian phylogenetics},
  author={Fan, Yu and Wu, Rui and Chen, Ming-Hui and Kuo, Lynn and Lewis, Paul O},
  journal={Molecular biology and evolution},
  volume={28},
  number={1},
  pages={523--532},
  year={2011},
  publisher={SMBE}
}

@article{Cook2006,
  title={Validation of software for {B}ayesian models using posterior quantiles},
  author={Cook, Samantha R and Gelman, Andrew and Rubin, Donald B},
  journal={Journal of Computational and Graphical Statistics},
  volume={15},
  number={3},
  year={2006}
}

@article{GelmanRubin1992,
  title={Inference from iterative simulation using multiple sequences},
  author={Gelman, Andrew and Rubin, Donald B},
  journal={Statistical science},
  pages={457--472},
  year={1992},
  publisher={JSTOR}
}

@article{Hohenlohe2008,
  title={{MIPoD}: a hypothesis-testing framework for microevolutionary inference from patterns of divergence},
  author={Hohenlohe, Paul A and Arnold, Stevan J},
  journal={The American Naturalist},
  volume={171},
  number={3},
  pages={366},
  year={2008},
  publisher={NIH Public Access}
}

@article{Felsenstein1988,
  title={Phylogenies and quantitative characters},
  author={Felsenstein, Joseph},
  journal={Annual Review of Ecology and Systematics},
  volume={19},
  pages={445--471},
  year={1988},
  publisher={JSTOR}
}

@article{Lynch1989,
  title={Phylogenetic hypotheses under the assumption of neutral quantitative-genetic variation},
  author={Lynch, Michael},
  journal={Evolution},
  pages={1--17},
  year={1989},
  publisher={JSTOR}
}

@article{Lynch1990,
  title={The rate of morphological evolution in mammals from the standpoint of the neutral expectation},
  author={Lynch, Michael},
  journal={American Naturalist},
  pages={727--741},
  year={1990},
  publisher={JSTOR}
}

@article{Turellietal1988,
  title={Rate tests for selection on quantitative characters during macroevolution and microevolution},
  author={Turelli, Michael and Gillespie, John H and Lande, Russell},
  journal={Evolution},
  volume={42},
  number={5},
  pages={1085--1089},
  year={1988},
  publisher={JSTOR}
}

@article{Felsenstein1985,
  title={Phylogenies and the comparative method},
  author={Felsenstein, Joseph},
  journal={American Naturalist},
  pages={1--15},
  year={1985},
  publisher={JSTOR}
}

@article{HansenBartoszek2012,
  title={Interpreting the evolutionary regression: the interplay between observational and biological errors in phylogenetic comparative studies},
  author={Hansen, Thomas F and Bartoszek, Krzysztof},
  journal={Systematic biology},
  volume={61},
  number={3},
  pages={413--425},
  year={2012},
  publisher={Oxford University Press}
}

@article{Lande19

repository: uyedaj/bmr

repo_name: uyedaj/bmr