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Charles R. Marshall - One of the best experts on this subject based on the ideXlab platform.
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when can decreasing diversification rates be detected with molecular phylogenies and the Fossil Record
Systematic Biology, 2010Co-Authors: Lee Hsiang Liow, Charles R. Marshall, Tiago B QuentalAbstract:Traditionally, patterns and processes of diversification could only be inferred from the Fossil Record. However, there are an increasing number of tools that enable diversification dynamics to be inferred from molecular phylogenies. The application of these tools to new data sets has renewed interest in the question of the prevalence of diversity-dependent diversification. However, there is growing recognition that the absence of extinct species in molecular phylogenies may prevent accurate inferences about the underlying diversification dynamics. On the other hand, even though the Fossil Record provides direct data on extinct species, its incompleteness can also mask true diversification processes. Here, using computer-generated diversity-dependent phylogenies, we mimicked molecular phylogenies by eliminating extinct lineages. We also simulated the Fossil Record by converting the temporal axis into discrete intervals and imposing a variety of preservation processes on the lineages. Given the lack of reliable phylogenies for many Fossil marine taxa, we also stripped away phylogenetic information from the computer-generated phylogenies. For the simulated molecular phylogenies, we examined the efficacy of the standard metric (the γ statistic) for identifying decreasing rates of diversification. We find that the underlying decreasing rate of diversification is detected only when the rate of change in the diversification rate is high, and if the molecular phylogeny happens to capture the diversification process as the equilibrium diversity is first reached or shortly thereafter. In contrast, estimating rates of diversification from the simulated Fossil Record captures the expected zero rate of diversification after equilibrium is reached under a wide range of preservation scenarios. The ability to detect the initial decreasing rate of diversification is lost as the temporal resolution of the Fossil Record drops and with a decreased quality of preservation. When the rate of change of the diversification rate is low, the γ statistic will typically fail to detect the decreasing rate of diversification, as will the Fossil Record, although the Fossil Record still retains the signature of the diversity dependence in yielding approximately zero diversification rates. Thus, although a significantly negative γ value for a molecular phylogeny indicates a decreasing rate of diversification, a nonsignificantly negative or positive γ value might mean exponential diversification, or a slowly decreasing rate of diversification, or simply species turnover at a constant diversity. The Fossil Record can be of assistance in helping choose among these possibilities.
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diversity dynamics molecular phylogenies need the Fossil Record
Trends in Ecology and Evolution, 2010Co-Authors: Tiago B Quental, Charles R. MarshallAbstract: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.
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phanerozoic marine biodiversity dynamics in light of the incompleteness of the Fossil Record
Proceedings of the National Academy of Sciences of the United States of America, 2006Co-Authors: Motohiro Yogo, Charles R. MarshallAbstract:Long-term evolutionary dynamics have been approached through quantitative analysis of the Fossil Record, but without explicitly taking its incompleteness into account. Here we explore the temporal covariance structure of per-genus origination and extinction rates for global marine Fossil genera throughout the Phanerozoic, both before and after corrections for the incompleteness of the Fossil Record. Using uncorrected data based on Sepkoski’s compendium, we find significant autocovariance within origination and extinction rates, as well as covariance between extinction and origination, not one, but two, intervals later, corroborating evidence for the unexplained temporal gap found by past studies. However, these effects vanish when the data are corrected for the incompleteness of the Fossil Record. Instead, we observe significant covariance only between extinction and origination in the immediately following intervals. The gap in the response of the biosphere to extinction in the uncorrected Fossil Record thus appears to be an artifact of the incompleteness of the Fossil Record, specifically due to episodic variation in the probability that taxa will be preserved, on time scales comparable to the temporal resolution of Sepkoski’s data. Our results also indicate that at that temporal resolution (the stage/substage of duration ≈5 million years), changes in origination and extinction do not persist for longer than one interval, except that elevated origination rates immediately after extinction may last for more than a single interval. Thus, although certain individual cases may deviate from the overall pattern, we find that in general the biosphere’s response to perturbation is immediate geologically and usually short-lived.
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A Framework for Analysing Fossil Record Data
Lecture Notes in Statistics, 2004Co-Authors: Robert E. Weiss, Sanjib Basu, Charles R. MarshallAbstract:This chapter focuses on a new approach to building chronologies on the basis of data from stratigraphic sequences of Fossil plants and /or animals sealed within geological deposits. In order to understand the speed and timing of changes within the Fossil Record, geologists have for many years made systematic studies of the nature and number of taxa present in geological sequences. However, due to the incompleteness of the Fossil Record, a particular taxon may not be observed even when it is extant at a particular sampling point. Sampling intensity can vary across sampling points by orders of magnitude, and, depending on appearances (originations) and extinctions, different taxa compete to become part of the sample. This chapter offers a Bayesian statistical framework for interpreting data of this type. Abundance and depth (or stratigraphic position) data are combined to estimate the times of appearances and disappearances of taxa in the presence of prior information including an estimated longevity of each taxon and the probability that it will be observed if extant.
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Distinguishing between sudden and gradual extinctions in the Fossil Record: Predicting the position of the Cretaceous-Tertiary iridium anomaly using the ammonite Fossil Record on Seymour Island, Antarctica
Geology, 1995Co-Authors: Charles R. MarshallAbstract:A simple method, employing 50% confidence intervals, may be used to distinguish sudden from gradual extinctions. In cases where the Fossil Record is consistent with a sudden disappearance, the expected position of the extinction horizon may als o be determined. Analysis of the Fossil ammonites on Seymour Island shows that their pattern of disappearances is consistent with a sudden mass extinction at the Cretaceous-Tertiary (K-T) boundary, even though a literal reading of the Fossil Record shows they disappeared gradually over a stratigraphic interval 10–50 m below the boundary. It is striking that the iridium anomaly on Seymour Island falls within the stratigraphic interval determined by the 50% confidence intervals to be the most likely place for the K-T boundary (assuming there was a sudden disappearance of ammonites at the boundary). However, a computer simulation of the Seymour Island ammonite Fossil Record indicates a wide range of other extinction scenarios, including gradual extinctions ranging over as much as 20 m (α = 0.05), that are consistent with the ammonite Fossil Record; without saturation collecting near the K-T boundary it will be impossible to distinguish between gradual and sudden extinction scenarios for the Seymour Island ammonites based on the ammonite Fossil Record alone.
Michael J. Benton - One of the best experts on this subject based on the ideXlab platform.
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Assessing the quality of the Fossil Record: insights from vertebrates
Geological Society London Special Publications, 2011Co-Authors: Michael J. Benton, Alexander M. Dunhill, Graeme T. Lloyd, Felix G. MarxAbstract:Assessing the quality of the Fossil Record is notoriously hard, and many recent attempts have used sampling proxies that can be questioned. For example, counts of geological formations and estimated outcrop areas might not be defensible as reliable sampling proxies: geological formations are units of enormously variable dimensions that depend on rock heterogeneity and Fossil content (and so are not independent of the Fossil Record), and outcrop areas are not always proportional to rock exposure, probably a closer indicator of rock availability. It is shown that in many cases formation counts will always correlate with Fossil counts, whatever the degree of sampling. It is not clear, in any case, that these proxies provide a good estimate of what is missing in the gap between the known Fossil Record and reality; rather they largely explore the gap between known and potential Fossil Records. Further, using simple, single numerical metrics to correct global-scale raw data, or to model sampling-driven patterns may be premature. There are perhaps four approaches to exploring the incompleteness of the Fossil Record, (1) regionalscale studies of geological completeness; (2) regionalor clade-scale studies of sampling completeness using comprehensive measures of sampling, such as numbers of localities or specimens or Fossil quality; (3) phylogenetic and gap-counting methods; and (4) model-based approaches that compare sampling as one of several explanatory variables with measures of environmental change, singly and in combination. We suggest that palaeontologists, like other scientists, should accept that their data are patchy and incomplete, and use appropriate methods to deal with this issue in each analysis. All that matters is whether the data are adequate for a designated study or not. A single answer to the question of whether the Fossil Record is driven by macroevolution or megabias is unlikely ever to emerge because of temporal, geographical, and taxonomic variance in the data. The Fossil Record is far from perfect, and palaeontologists must be concerned about inadequacy and bias (Raup 1972; Benton 1998; Smith 2001, 2007a). Fundamental issues concerning the quality and completeness of the Fossil Record were enunciated clearly by Charles Darwin (1859, pp. 287–288), who wrote: That our palaeontological collections are very imperfect, is admitted by every one. The remark of that admirable palaeontologist, the late Edward Forbes, should not be forgotten, namely, that numbers of our Fossil species are known and named from single and often broken specimens, or from a few specimens collected on some one spot. Only a small portion of the surface of the earth has been geologically explored, and no part with sufficient care, as the important discoveries made every year in Europe prove. No organism wholly soft can be preserved. Shells and bones will decay and disappear when left on the bottom of the sea, where sediment is not accumulating. . . With respect to the terrestrial productions which lived during the Secondary and Palaeozoic periods, it is superfluous to state that our evidence from Fossil remains is fragmentary in an extreme degree. Raup (1972) clarified the situation when he compared the ‘empirical’ model of Valentine (1969), a literal reading of the Fossil Record, with his ‘bias simulation model’ that explained the bulk of the apparent low diversity levels of marine invertebrates in the Palaeozoic as a sampling error. Two opposite viewpoints have been argued, either that the Fossil Record is good enough (e.g. Sepkoski et al. 1981; Benton 1995; Benton et al. 2000; Stanley 2007) or not good enough (e.g. Raup 1972; Alroy et al. 2001, 2008; Peters & Foote 2002; Alroy 2010) to show the main patterns of global diversification through time. A resolution between these opposite viewpoints does not appear close (Benton 2009; Erwin 2009; Marshall 2010). From: McGowan, A. J. & Smith, A. B. (eds) Comparing the Geological and Fossil Records: Implications for Biodiversity Studies. Geological Society, London, Special Publications, 358, 63–94. DOI: 10.1144/SP358.6 0305-8719/11/$15.00 # The Geological Society of London 2011. Key objective evidence for bias in the Fossil Record could be the extraordinary and ubiquitous correlation of sampling proxies and diversity curves: why is there such close tracking of measures of rock volume by palaeodiversity? There are three possible explanations: (1) rock volume/sampling drives the diversity signal (Peters & Foote 2001, 2002; Smith 2001, 2007a; Butler et al. 2011); (2) both signals reflect a third, or ‘common’, cause such as sea-level fluctuation (Peters 2005; Peters & Heim 2010); or (3) both signals are entirely or partially redundant (1⁄4 identical) with each other. In reality, the close correlation probably reflects a combination of all three factors in different proportions in any test case, and so it is probably fruitless to prolong the debate about which of the three models is correct, and which incorrect. Much of the literature on the quality of the rock and Fossil Records has focused on marine settings. This reflects the interests of palaeontologists who engage with these questions, and the fact that many marine rock Records are more complete than most terrestrial (continental) rock Records. However, the terrestrial Fossil Record is worth considering for several reasons: terrestrial life today is much more diverse than marine life, perhaps representing 85% of modern biodiversity (May 1990; Vermeij & Grosberg 2010), terrestrial life includes many major taxa that are sensitive to atmospheric, temperature, and topographic change and so are key indicator species in studies of global change, and for many terrestrial groups (e.g. angiosperms, insects, vertebrates) there are mature morphological and molecular phylogenies that enable cross-comparison between stratigraphic and cladistic data. In this paper, we explore the use of sampling proxies, and suggest that some commonly used measures, notably formation counts and outcrop areas, may not be useful or accurate measures of sampling. Indeed, we suggest that there is probably no single numerical metric that captures all aspects of sampling (1⁄4 rock volume, accessibility, effort), and recent attempts to correct the raw data, or to model sampling-driven patterns, may be premature. We then look at some case studies of patchy Fossil Records in taxa with good phylogenetic data, and suggest that in some cases at least the rock volume and Fossil occurrence measures are identical, and so correlate almost perfectly. Finally, we suggest that such global-scale confrontations of sampling proxies and Fossil data are not adequate at present, and recommend instead study-scale approaches to detect and correct sampling, involving direct evidence for missing data (e.g. Lazarus taxa; ghost ranges), direct evidence for sampling (e.g. number of localities or samples per time bin; Fossil specimen completeness), and an integrated, model-based approach to incorporating sampling and explanatory models into explaining particular diversity curves. The Fossil Record, reality and sampling The Fossil Record, collector curves and
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The completeness of the Fossil Record
Significance, 2009Co-Authors: Michael J. BentonAbstract:Fossils are the data for evolution. The Fossil Record was already well known 150 years ago, when Charles Darwin published On the Origin of Species, and it is central to Darwin's theories; yet it is commonly claimed that the Fossil Record is woefully incomplete. Creationists say that it does not show the missing links that evolution predicts. Michael Benton asks if the gaps are too big to fill in.
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eLS - Fossil Record: Quality
Encyclopedia of Life Sciences, 2005Co-Authors: Michael J. BentonAbstract:There are divergent opinions about the quality of the Fossil Record and its ability to give a useful representation of the history of life. Extensive testing, by comparisons of the congruence of morphological and molecular phylogenies, suggests that the Fossils do tell the story relatively well. Keywords: Fossils; quality; completeness
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Speciation in the Fossil Record
Trends in ecology & evolution, 2001Co-Authors: Michael J. Benton, Paul Nicholas PearsonAbstract:It is easy to claim that the Fossil Record says nothing about speciation because the biological species concept (which relies on interbreeding) cannot be applied to it and genetic studies cannot be carried out on it. However, Fossilized organisms are often preserved in sufficient abundance for populations of intergrading morphs to be recognized, which, by analogy with modern populations, are probably biological species. Moreover, the Fossil Record is our only reliable documentation of the sequence of past events over long time intervals: the processes of speciation are generally too slow to be observed directly, and permanent reproductive isolation can only be verified with hindsight. Recent work has shown that some parts of the Fossil Record are astonishingly complete and well documented, and patterns of lineage splitting can be examined in detail. Marine plankton appear to show gradual speciation, with subsequent morphological differentiation of lineages taking up to 500 000 years to occur. Marine invertebrates and vertebrates more commonly show punctuated patterns, with periods of rapid speciation followed by long-term stasis of species lineages.
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The Fossil Record of Cretaceous Tetrapods
PALAIOS, 2000Co-Authors: Emmanuel Fara, Michael J. BentonAbstract:Abstract The Fossil Record of the Cretaceous is critical for understanding the evolution of modern tetrapods. Using a measure of relative completeness of the Fossil Record—the Simple Completeness Metric (SCM)—quality of the Fossil Record and diversity during the Cretaceous appear to be closely related, suggesting an artifactual component. The SCM calculations also show that knowledge of the Fossil Record has improved in the last ten years. Recent proposals that modern orders of birds and mammals originated early in the Cretaceous are rendered unlikely by four arguments: (1) the SCM calculations indicate that the Fossil Record of Cretaceous birds and mammals is relatively good; (2) it is unlikely that all modern orders, independently, would have remained cryptic throughout the Cretaceous; (3) control samples of exquisitely preserved tiny Cretaceous tetrapods lack any specimens of modern groups of birds and mammals; and (4) the suggestion that the undiscovered ancestors of modern groups are to be found in u...
Tiago B Quental - One of the best experts on this subject based on the ideXlab platform.
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when can decreasing diversification rates be detected with molecular phylogenies and the Fossil Record
Systematic Biology, 2010Co-Authors: Lee Hsiang Liow, Charles R. Marshall, Tiago B QuentalAbstract:Traditionally, patterns and processes of diversification could only be inferred from the Fossil Record. However, there are an increasing number of tools that enable diversification dynamics to be inferred from molecular phylogenies. The application of these tools to new data sets has renewed interest in the question of the prevalence of diversity-dependent diversification. However, there is growing recognition that the absence of extinct species in molecular phylogenies may prevent accurate inferences about the underlying diversification dynamics. On the other hand, even though the Fossil Record provides direct data on extinct species, its incompleteness can also mask true diversification processes. Here, using computer-generated diversity-dependent phylogenies, we mimicked molecular phylogenies by eliminating extinct lineages. We also simulated the Fossil Record by converting the temporal axis into discrete intervals and imposing a variety of preservation processes on the lineages. Given the lack of reliable phylogenies for many Fossil marine taxa, we also stripped away phylogenetic information from the computer-generated phylogenies. For the simulated molecular phylogenies, we examined the efficacy of the standard metric (the γ statistic) for identifying decreasing rates of diversification. We find that the underlying decreasing rate of diversification is detected only when the rate of change in the diversification rate is high, and if the molecular phylogeny happens to capture the diversification process as the equilibrium diversity is first reached or shortly thereafter. In contrast, estimating rates of diversification from the simulated Fossil Record captures the expected zero rate of diversification after equilibrium is reached under a wide range of preservation scenarios. The ability to detect the initial decreasing rate of diversification is lost as the temporal resolution of the Fossil Record drops and with a decreased quality of preservation. When the rate of change of the diversification rate is low, the γ statistic will typically fail to detect the decreasing rate of diversification, as will the Fossil Record, although the Fossil Record still retains the signature of the diversity dependence in yielding approximately zero diversification rates. Thus, although a significantly negative γ value for a molecular phylogeny indicates a decreasing rate of diversification, a nonsignificantly negative or positive γ value might mean exponential diversification, or a slowly decreasing rate of diversification, or simply species turnover at a constant diversity. The Fossil Record can be of assistance in helping choose among these possibilities.
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diversity dynamics molecular phylogenies need the Fossil Record
Trends in Ecology and Evolution, 2010Co-Authors: Tiago B Quental, Charles R. MarshallAbstract: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.
Michel Laurin - One of the best experts on this subject based on the ideXlab platform.
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The reconstructed evolutionary process with the Fossil Record
Journal of theoretical biology, 2012Co-Authors: Gilles Didier, Manuela Royer-carenzi, Michel LaurinAbstract:Using the Fossil Record yields more detailed reconstructions of the evolutionary process than what is obtained from contemporary lineages only. In this work, we present a stochastic process modeling not only speciation and extinction, but also Fossil finds. Next, we derive an explicit formula for the likelihood of a reconstructed phylogeny with Fossils, which can be used to estimate the speciation and extinction rates. Finally, we provide a comparative simulation-based evaluation of the accuracy of estimations of these rates from complete phylogenies (including extinct lineages), from reconstructions with contemporary lineages only and from reconstructions with contemporary lineages and the Fossil Record. Results show that taking the Fossil Record into account yields more accurate estimates of speciation and extinction rates than considering only contemporary lineages.
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The reconstructed evolutionary process with the Fossil Record
Journal of Theoretical Biology, 2012Co-Authors: Gilles Didier, Manuela Royer-carenzi, Michel LaurinAbstract:We give a model of the reconstructed process from extant taxa and the Fossil Record. We show that it is a nonhomogeneous birth-and-death process. Its rates are expressed from time and speciation, extinction and Fossil find rates. We give a formula for the likelihood of a realization of this reconstructed process. Simulations show that Fossils improve speciation and extinction rate estimates. Using the Fossil Record yields more detailed reconstructions of the evolutionary process than what is obtained from contemporary lineages only. In this work, we present a stochastic process modeling not only speciation and extinction, but also Fossil finds. Next, we derive an explicit formula for the likelihood of a reconstructed phylogeny with Fossils, which can be used to estimate the speciation and extinction rates. Finally, we provide a comparative simulation-based evaluation of the accuracy of estimations of these rates from complete phylogenies (including extinct lineages), from reconstructions with contemporary lineages only and from reconstructions with contemporary lineages and the Fossil Record. Results show that taking the Fossil Record into account yields more accurate estimates of speciation and extinction rates than considering only contemporary lineages.
Gerhard C. Cadée - One of the best experts on this subject based on the ideXlab platform.
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Predator-Prey Interactions in the Fossil Record
Ichnos, 2005Co-Authors: Gerhard C. CadéeAbstract:Predator-Prey Interactions in the Fossil Record, edited by Patricia H. Kelley, Michal Kowalewski and Thor A. Hansen, 2003. Topics in Geobiology, volume 20, xvi + 464 p., Kluwer Academic/Plenum Publ...
