bioRxiv (Cold Spring Harbor Laboratory), Apr 13, 2024
Punctuated Equilibrium predicts a distribution of anatomical change that is fundamentally differe... more Punctuated Equilibrium predicts a distribution of anatomical change that is fundamentally different from the models used in studies of relationships among species. We present a model to assess relationships that assumes punctuated change. We apply this model to a dataset of strophomenoid brachiopods to demonstrate that a model of punctuated change fits better than a model of continuous-time ("phyletic gradualism") change in this group. Notably, because the punctuated model posits elevated speciation rates early in the strophomenoid history, the model also posits elevated rates of change among the early strophomenoids relative to later ones. This corroborates notions for what causes bursts of anatomical evolution rooted in ecological theory rather than evolutionary developmental theory. More basically, it emphasizes that paleontologists should consider both punctuated and continuous-time models when assessing relationships and other aspects of macroevolutionary theory.
I n tr -a ||f I Ppj • a*' tAjfy. j vi J UK ri Cl ^4' . \ J m J1 K ! Ifi f j wT lllr/^7 V M VO \\ ... more I n tr -a ||f I Ppj • a*' tAjfy. j vi J UK ri Cl ^4' . \ J m J1 K ! Ifi f j wT lllr/^7 V M VO \\ W SERIES PUBLICATIONS OF THE SMITHSONIAN INSTITUTION Emphasis upon publication as a means of "diffusing knowledge" was expressed by the first Secretary of the Smithsonian. In his formal plan for the Institution, Joseph Henry outlined a program that included the following statement: "It is proposed to publish a series of reports, giving an account of the new discoveries in science, and of the changes made from year to year in all branches of knowledge." This theme of basic research has been adhered to through the years by thousands of titles issued in series publications under the Smithsonian imprint, commencing with Smithsonian Contributions to Knowledge in 1848 and continuing with the following active series: Smithsonian Contributions to Anthropology Smithsonian Contributions to Botany Smithsonian Contributions to the Earth Sciences Smithsonian Contributions to the Marine Sciences Smithsonian Contributions to Paleobiology Smithsonian Contributions to Zoology Smithsonian Folklife Studies Smithsonian Studies in Air and Space Smithsonian Studies in History and Technology In these series, the Institution publishes small papers and full-scale monographs that report the research and collections of its various museums and bureaux or of professional colleagues in the world of science and scholarship. The publications are distributed by mailing lists to libraries, universities, and similar institutions throughout the world. Papers or monographs submitted for series publication are received by the Smithsonian Institution Press, subject to its own review for format and style, only through departments of the various Smithsonian museums or bureaux, where the manuscripts are given substantive review. Press requirements for manuscript and art preparation are outlined on the inside back cover.
Fossil Plant Relative Abundances Indicate Sudden Loss of Late Triassic Biodiversity in East Greenland
Science, 2009
Extinction Distinction The Triassic-Jurassic extinction approximately 200 million years ago is on... more Extinction Distinction The Triassic-Jurassic extinction approximately 200 million years ago is one of the five major extinctions in Earth's history. It has been primarily recognized through the loss of marine species, as well as the subsequent emergence of dinosaurs, but its pace, both on land and in sea, has been unclear. McElwain et al. (p. 1554 ) now provide evidence from the plant fossil record from rocks in East Greenland. The total number of taxa and the number of common taxa decreased across the extinction boundary. The decrease was fairly abrupt and seemed to coincide with a period with increased atmospheric CO 2 levels.
A long-running debate over the affinities of the Neoproterozoic 'Ediacara biota' has led ... more A long-running debate over the affinities of the Neoproterozoic 'Ediacara biota' has led to contrasting interpretations of Ediacaran ecosystem complexity. A 'simple' model assumes that most, if not all, Ediacaran organisms shared similar basic ecologies. A contrasting 'complex' model suggests that the Ediacara biota more likely represent organisms from a variety of different positions on the eukaryotic tree and thus occupied a wide range of different ecologies. We perform a quantitative test of Ediacaran ecosystem complexity using rank abundance distributions (RADs). We show that the Ediacara biota formed complex-type communities throughout much of their stratigraphic range and thus likely comprised species that competed for different resources and/or created niche for others ('ecosystem engineers'). One possible explanation for this pattern rests in the recent inference of multiple metazoan-style feeding modes among the Ediacara biota; in this scenar...
Question: Holding both the true number of taxa and their evenness constant, what is the effect of... more Question: Holding both the true number of taxa and their evenness constant, what is the effect of the shape of the abundance distribution on the number of sampled taxa? Method: We examine the effects of three types of abundance distribution (geometric, log-normal and Zipf) on the expected number of sampled taxa using Hurlbert's equation (1971, equation 14). First, we examine the differences in the number of sampled taxa for the three distributions given the same true number of taxa and true evenness. Second, we determine the sample ...
With or without realizing it, macroecology, paleobiology and conservation biology have been addre... more With or without realizing it, macroecology, paleobiology and conservation biology have been addressing similar issues using similar methods and analogous data sets. Much of what we call "paleobiology" overlaps heavily with macroecology, and their shared interest in losses in biodiversity over space and time clearly is of interest to conservation biology. Here we examine how some "classic" macroecological and paleobiological studies and techniques apply to issues that currently are of interest to conservation biology. Our examples are far from exhaustive, but include examining temporal (or possible temporal) shifts in: 1) geographic range sizes; 2) body size distributions; 3) relative abundance distributions; and, 4) morphological diversity. Reframing these issues in terms of how loss of biodiversity and richness affects particular slices of time including (but not limited to) the present should do much to communicate the value of macroecological and paleobiological methods and theory to conservation research.
Proceedings of the Royal Society B: Biological Sciences, 2021
We employ modified tip-dating methods to date divergence times within the Strophomenoidea, one of... more We employ modified tip-dating methods to date divergence times within the Strophomenoidea, one of the most abundant and species-rich brachiopod clades to radiate during the Great Ordovician Biodiversification Event (GOBE), to determine if significant environmental changes at this time correlate with the diversification of the clade. Models using origination, extinction and sampling rates to estimate prior probabilities of divergence times strongly support both high rates of anatomical change per million years and rapid divergences shortly before the clade first appears in the fossil record. These divergence times indicate much higher rates of cladogenesis than are typical of brachiopods during this interval. The correspondence of high speciation rates and high anatomical disparity suggests punctuated (speciational) change drove the high frequencies of early anatomical change, which in turn suggests increased ecological opportunities rather than shifting developmental constraints acc...
Testing character-evolution models in phylogenetic paleobiology: a case study with Cambrian echinoderms
Macroevolutionary inference has historically been treated as a two-step process, involving the in... more Macroevolutionary inference has historically been treated as a two-step process, involving the inference of a phylogenetic tree, and then inference of a macroevolutionary model using that tree. Newer models, such as the fossilized birth-death model, blend the two steps. These methods make more complete use of fossils than the previous generation of Bayesian phylogenetic models. They also involve many more parameters than prior models, including parameters about which empiricists may have little intuition. In this paper, we set forth a framework for fitting complex, hierarchical models.We ultimately fit and use a joint tree and diversification model to estimate a dated phylogeny of the Cincta (Echinodermata), a morphologically distinct group of Cambrian echinoderms that lack the five-fold radial symmetry characteristic of extant members of the phylum. Although the phylogeny of cinctans remains poorly supported in places, we show how models of character change and diversification cont...
Ecologists are increasingly using the fossil record of mass extinction to build predictive models... more Ecologists are increasingly using the fossil record of mass extinction to build predictive models for the ongoing biodiversity crisis. During mass extinctions, major depletions in global (i.e., gamma) diversity may reflect decrease in alpha diversity (i.e., local assemblages support fewer taxa), and/or decrease in beta diversity (such that similar pools of taxa are common to a greater number of local areas). Contrasting the effects of extinction on alpha and beta diversity is therefore central to understanding how global richness becomes depleted over these critical events. Here we investigate the spatial effects of mass extinction by examining changes in alpha, beta, and gamma diversity in brachiopod communities over both pulses of Ordovician-Silurian extinction (;445.2 and ;438.8 million years ago), which had dramatically different causal mechanisms. We furthermore reconstruct geographic range sizes for brachiopod genera to test competing models for drivers of beta diversity change. We find that: (1) alpha and beta diversity respond differently to extinction; (2) these responses differ between pulses of extinction; (3) changes in beta diversity associated with extinction are accompanied by changes in geographic range size; and (4) changes in global beta diversity were driven by the extinction of taxa with statistically small and large ranges, rather than range expansion/contraction in taxa that survive into the aftermath. A symptom of ongoing biotic crisis may therefore be the extinction of specific narrow-or wide-ranging taxa, rather than the global proliferation of opportunistic and ''disaster'' forms. In addition, our results illustrate that changes in beta diversity on these longer timescales may largely be dictated by emplacement and removal of barriers to dispersal. Lastly, this study reinforces the utility of the fossil record in addressing questions surrounding the role of global-scale processes (such as mass extinctions) in sculpting and assembling regional biotas.
Proceedings of the National Academy of Sciences of the United States of America, Jan 18, 2014
Evolution provides many cases of apparent shifts in diversification associated with particular an... more Evolution provides many cases of apparent shifts in diversification associated with particular anatomical traits. Three general models connect these patterns to anatomical evolution: (i) elevated net extinction of taxa bearing particular traits, (ii) elevated net speciation of taxa bearing particular traits, and (iii) elevated evolvability expanding the range of anatomies available to some species. Trait-based diversification shifts predict elevated hierarchical stratigraphic compatibility (i.e., primitive→derived→highly derived sequences) among pairs of anatomical characters. The three specific models further predict (i) early loss of diversity for taxa retaining primitive conditions (elevated net extinction), (ii) increased diversification among later members of a clade (elevated net speciation), and (iii) increased disparity among later members in a clade (elevated evolvability). Analyses of 319 anatomical and stratigraphic datasets for fossil species and genera show that hierarc...
The biogeographical distribution of Ordovician and Silurian gastropods, monoplacophorans and mimo... more The biogeographical distribution of Ordovician and Silurian gastropods, monoplacophorans and mimospirids has been analysed on a generic level. The dataset contains 334 genera and 2769 species, yielding 1231 records of genera with 2274 occurrences worldwide. There is a bias towards eastern Laurentia, Baltica and Perunica records. Some 53.1% of the records are Ordovician. The study demonstrates that these molluscs are well suited to being used to improve understanding of Ordovician and Silurian biogeographical provinciality. Specific points are that: a Lower Ordovician assemblage is evident in Laurentia; the fauna of the Argentinean Precordillera is Laurentian until the Darriwilian, when taxa are shared with North China; Late Silurian gastropods from the Alexander terrane (SE Alaska) are unknown in Laurentia, but support a rift origin of this terrane from NE Siberia; Perunica, Ibero-Armorica and Morocco cluster together throughout the Ordovician but Perunica and Morocco are closer; Darriwilian-Sandbian deep-water Bohemian taxa occur in Baltica; a Laurentian-Baltica proximity is unsupported until the Silurian; Siberia clusters with North China and eastern Laurentia during the Tremadocian-Darriwilian; during the Gorstian-Pridoli Siberia clusters with the Farewell and Alexander terranes; North China may have been close to Laurentia and the Argentinean margin of Gondwana; and the affinity of Tarim taxa is problematic.
Proceedings of the National Academy of Sciences, 2001
Global diversity curves reflect more than just the number of taxa that have existed through time:... more Global diversity curves reflect more than just the number of taxa that have existed through time: they also mirror variation in the nature of the fossil record and the way the record is reported. These sampling effects are best quantified by assembling and analyzing large numbers of locality-specific biotic inventories. Here, we introduce a new database of this kind for the Phanerozoic fossil record of marine invertebrates. We apply four substantially distinct analytical methods that estimate taxonomic diversity by quantifying and correcting for variation through time in the number and nature of inventories. Variation introduced by the use of two dramatically different counting protocols also is explored. We present sampling-standardized diversity estimates for two long intervals that sum to 300 Myr (Middle Ordovician-Carboniferous; Late Jurassic-Paleogene). Our new curves differ considerably from traditional, synoptic curves. For example, some of them imply unexpectedly low late Cr...
The notion that two characters evolve independently is of interest for two reasons. First, theori... more The notion that two characters evolve independently is of interest for two reasons. First, theories of biological integration often predict that change in one character requires complementary change in another. Second, character independence is a basic assumption of most phylogenetic inference methods, and dependent characters might confound attempts at phylogenetic inference. Previously proposed tests of correlated character evolution require a model phylogeny and therefore assume that nonphylogenetic correlation has a negligible effect on initial tree construction. This paper develops "tree-free" methods for testing the independence of cladistic characters. These methods can test the character independence model as a hypothesis before phylogeny reconstruction, or can be used simply to test for correlated evolution. We rst develop an approach for visualizin g suites of correlated characters by using character compatibility. Two characters are compatible if they can be used to construct a tree without homoplasy. The approach is based on the examination of mutual compatibilitie s between characters. The number of times two characters i and j share compatibility with a third character is calculated, and a pairwise shared compatibility matrix is constructed. From this matrix, an association matrix analogous to a dissimilarity matrix is derived. Eigenvector analyses of this association matrix reveal suites of characters with similar compatibility patterns. A priori character subsets can be tested for signi cant correlation on these axes. Monte Carlo tests are performed to determine the expected distribution of mutual compatibilities , given various criteria from the original data set. These simulated distributions are then used to test whether the observed amounts of nonphylogenetic correlation in character suites can be attributed to chance alone. We have applied these methods to published morphological data for caecilian amphibians. The analyses corroborate instances of dependent evolution hypothesized by previous workers and also identify novel partitions. Phylogenetic analysis is performed after reducing correlated suites to single characters. The resulting cladogram has greater topological resolution and implies appreciably less change among the remaining characters than does a tree derived from the raw data matrix. [Character independence; character weighting; compatibility; correlated character evolution; similarity coef cient.]
Proceedings of the Royal Society B: Biological Sciences, 2007
Occurrence-based databases such as the Palaeobiology database (PBDB) provide means of accommodati... more Occurrence-based databases such as the Palaeobiology database (PBDB) provide means of accommodating the heterogeneities of the fossil record when evaluating historical diversity patterns. Although palaeontologists have given ample attention to the effects of taxonomic practice on diversity patterns derived from synoptic databases (those using first and last appearances of taxa), workers have not examined the effects of taxonomic error on occurrence-based diversity studies. Here, we contrast diversity patterns and diversity dynamics between raw data and taxonomically vetted data in the PBDB to evaluate the effects of taxonomic errors. We examine three groups: Palaeozoic gastropods, Jurassic bivalves and Cenozoic bivalves. We contrast genus-level diversity patterns based on: (i) all occurrences assigned to a genus (i.e. both species records and records identifying only the genus), (ii) only occurrences for which a species is identified, and (iii) only occurrences for which a species i...
Philosophical Transactions of the Royal Society B: Biological Sciences, 2010
Understanding and predicting how species' distributions will shift as climate changes are cen... more Understanding and predicting how species' distributions will shift as climate changes are central questions in ecology today. The late Quaternary of North America represents a natural experiment in which we can evaluate how species responded during the expansion and contraction of the glaciers. Here, we ask whether species' range shifts differ because of taxonomic affinity, life-history traits, body size or topographic heterogeneity and whether the species survived the megafaunal extinction. There was no difference in range shifts between victims and survivors of the megafaunal extinction. In general, the change in the size of a species' range is not well correlated with any of the ecological or life-history traits evaluated. However, there are significant relationships between some variables and the movements of the centroids of ranges. Differences in the distances shifted exist among orders, although this is probably a result of body size differences as larger bodied s...
Phanerozoic trends in shell and life habit traits linked to postmortem durability were evaluated ... more Phanerozoic trends in shell and life habit traits linked to postmortem durability were evaluated for the most common fossil brachiopod, gastropod, and bivalve genera in order to test for changes in taphonomic bias. Using the Paleobiology Database, we tabulated occurrence frequencies of genera for 48 intervals of ∼11 Myr duration. The most frequently occurring genera, cumulatively representing 40% of occurrences in each time bin, were scored for intrinsic durability on the basis of shell size, reinforcement (ribs, folds, and spines), life habit, and mineralogy.Shell durability is positively correlated with the number of genera in a time bin, but durability traits exhibit different temporal patterns across higher taxa, with notable offsets in the timing of changes in these traits. We find no evidence for temporal decreases in durability that would indicate taphonomic bias at the Phanerozoic scale among commonly occurring genera. Also, all three groups show a remarkable stability in me...
Previous studies of overall arthropod disparity have compared Cambrian and Recent biotas, without... more Previous studies of overall arthropod disparity have compared Cambrian and Recent biotas, without considering taxa of intermediate age. This study explored morphological diversity among Carboniferous arthropods, primarily from the well-known Westphalian Mazon Creek Lagerstä tte. Over 100 arthropod species, belonging to 48 orders, were examined. The data set is composed of nearly equal numbers of crustacean, arachnid, and insect species, with lower numbers of merostomes. Trilobites have not been found at Mazon Creek. However, some Late Carboniferous trilobite species were included in order to obtain a more representative picture of global Carboniferous arthropod disparity. The absence, presence, or state of 66 shared characters was recorded for each species, as well as individual autapomorphies. Overall disparity was determined from the Euclidean distance analysis between taxa or variance along principal coordinates analyses (PCO) axes. Results indicate that arthropod disparity has not been greatly reduced throughout the Phanerozoic as was previously suggested. However, the regions of occupied morphospace have rotated over time.
Uploads
Papers by Peter Wagner