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Thomas J. M. Schopf

Bio: Thomas J. M. Schopf is an academic researcher from University of Chicago. The author has contributed to research in topics: Genetic variability & Punctuated equilibrium. The author has an hindex of 23, co-authored 50 publications receiving 4803 citations.

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TL;DR: This work has extended the use of equilibrium models to examine patterns of phyletic diversification in the fossil record and generated evolutionary trees by stochastic simulation and classified their lineages into clades.
Abstract: Equilibrium models in population biology have demonstrated that accurate predictions of species diversity can be made without reference to particular taxa. We have extended the use of equilibrium models to examine patterns of phyletic diversification in the fossil record. We assume that (1) regions become saturated with respect to the number of taxa that can coexist; and (2) after that limit is reached, rates of speciation and extinction are very similar. Using these minimal constraints, and the standard precepts of evolutionary taxonomy (monophyly), we have generated evolutionary trees by stochastic simulation and classified their lineages into clades. Random processes with minimal constraints yield phyletic trees similar to those based upon the fossil record. Of particular interest are the patterns of clade origination and extinction and of intraclade diversity. For comparison with computer simulations, we present actual clades for the Reptilia. The similarities are striking, but some patterns of the fo...

512 citations

Journal ArticleDOI
TL;DR: A random model that builds evolutionaiy trees by allowing lineages to branch and become extinct at equal probabilities is constructed, and the similarity of real and random clades is regarded as the outstanding result of this work.
Abstract: The history of life is replete with apparent order. Much of this order may reflect the deterministic causes conventionally invoked, but we cannot be sure until we measure and subtract the order that arises in simple random systems. Consequently, we have constructed a random model that builds evolutionary trees by allowing lineages to branch and become extinct at equal probabilities. We proceed by dividing our simulated tree into clades and by comparing their sizes and shapes with the patterns exhibited by “real” clades as recorded by fossils.We regard the similarity of real and random clades as the outstanding result of this comparison. In both real and random systems, extinct clades arising after an “ecological barrel” had been filled have their maximum diversity at the midpoint of their duration; clades arising during the initial “filling” reach an earlier climax during this preequilibrial period of rapid diversification. However, some potential differences also emerge. Clades still living are much larger than extinct clades. We may attribute this to the morphological superiority of survivors, but we can also simulate it in a model that chooses the originators of clades at random. Real clades undergo greater fluctuations in diversity than do random clades, but the effect is not marked.

290 citations

Journal ArticleDOI
Abstract: An analysis of the Permo-Triassic fauna and paleogeography on a stage-by-stage basis supports previous more general summaries by concluding that the number of families of marine invertebrates was significantly reduced (essentially halved) during the last three Permian stages (32 m.y.), and that the extinctions were not markedly selective. Shallow marine seas were reduced from a coverage of 40% of their possible distribution in the early Permian to less than 15% coverage in latest Permian, and then were expanded to 34% coverage in the lower Triassic. If this apparent reduction in shallow marine seas is due to selective erosion of late Permian sediments, there seems no way to account for it unless there was significant reduction in sea level. Alternatively, late Permian marine seas may never have been widespread, again due to lowering of sea level. The apparent late Permian marine regression is attributed to water withdrawing into a deepening ocean basin. The basaltic ocean bottom continued to sink during a...

162 citations


Cited by
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TL;DR: Preface to the Princeton Landmarks in Biology Edition vii Preface xi Symbols used xiii 1.
Abstract: Preface to the Princeton Landmarks in Biology Edition vii Preface xi Symbols Used xiii 1. The Importance of Islands 3 2. Area and Number of Speicies 8 3. Further Explanations of the Area-Diversity Pattern 19 4. The Strategy of Colonization 68 5. Invasibility and the Variable Niche 94 6. Stepping Stones and Biotic Exchange 123 7. Evolutionary Changes Following Colonization 145 8. Prospect 181 Glossary 185 References 193 Index 201

14,171 citations

Journal Article
TL;DR: For the next few weeks the course is going to be exploring a field that’s actually older than classical population genetics, although the approach it’ll be taking to it involves the use of population genetic machinery.
Abstract: So far in this course we have dealt entirely with the evolution of characters that are controlled by simple Mendelian inheritance at a single locus. There are notes on the course website about gametic disequilibrium and how allele frequencies change at two loci simultaneously, but we didn’t discuss them. In every example we’ve considered we’ve imagined that we could understand something about evolution by examining the evolution of a single gene. That’s the domain of classical population genetics. For the next few weeks we’re going to be exploring a field that’s actually older than classical population genetics, although the approach we’ll be taking to it involves the use of population genetic machinery. If you know a little about the history of evolutionary biology, you may know that after the rediscovery of Mendel’s work in 1900 there was a heated debate between the “biometricians” (e.g., Galton and Pearson) and the “Mendelians” (e.g., de Vries, Correns, Bateson, and Morgan). Biometricians asserted that the really important variation in evolution didn’t follow Mendelian rules. Height, weight, skin color, and similar traits seemed to

9,847 citations

Journal ArticleDOI
TL;DR: A common pattern of phylogenetic conservatism in ecological character is recognized and the challenges of using phylogenies of partial lineages are highlighted and phylogenetic approaches to three emergent properties of communities: species diversity, relative abundance distributions, and range sizes are reviewed.
Abstract: ▪ Abstract As better phylogenetic hypotheses become available for many groups of organisms, studies in community ecology can be informed by knowledge of the evolutionary relationships among coexisting species. We note three primary approaches to integrating phylogenetic information into studies of community organization: 1. examining the phylogenetic structure of community assemblages, 2. exploring the phylogenetic basis of community niche structure, and 3. adding a community context to studies of trait evolution and biogeography. We recognize a common pattern of phylogenetic conservatism in ecological character and highlight the challenges of using phylogenies of partial lineages. We also review phylogenetic approaches to three emergent properties of communities: species diversity, relative abundance distributions, and range sizes. Methodological advances in phylogenetic supertree construction, character reconstruction, null models for community assembly and character evolution, and metrics of community ...

3,615 citations

Journal ArticleDOI
TL;DR: This poster presents a probabilistic procedure to characterize the response of the immune system to E.coli bacteria and shows clear patterns in response to the presence of E. coli.
Abstract: 1Department of Genetics, University of Georgia, Athens, Georgia 30602; 2NMFS/ CZES, Genetics, 2725 Montlake Boulevard East, Seattle, Washington 98112; 3Savannah River Ecology Laboratory, Drawer E, Aiken, South Carolina 29801; ~Department of Microbiology and Immunology, School of Medicine, University of California, Los Angeles, California 90024; -SSchool f Veterinary Medicine, Virginia Tech University, Blacksburg, Virginia 24046

3,366 citations

Journal ArticleDOI
TL;DR: It is argued that virtually none of the examples brought forward to refute the model of punctuated equilibria 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.
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.

2,278 citations