scholarly journals A Bayesian Approach for Detecting Mass-Extinction Events When Rates of Lineage Diversification Vary

2015 ◽  
Author(s):  
Michael R. May ◽  
Sebastian Höhna ◽  
Brian R. Moore
Keyword(s):  
Mass Extinction ◽  
Process Model ◽  
Sequence Data ◽  
Diversification Rate ◽  
Rate Variation ◽  
Specific Rate ◽  
Extinction Rate ◽  
Molecular Sequence Data ◽  
Extinction Events ◽  
Mass Extinction Events

The paleontological record chronicles numerous episodes of mass extinction that severely culled the Tree of Life. Biologists have long sought to assess the extent to which these events may have impacted particular groups. We present a novel method for detecting mass-extinction events from phylogenies estimated from molecular sequence data. We develop our approach in a Bayesian statistical framework, which enables us to harness prior information on the frequency and magnitude of mass-extinction events. The approach is based on an episodic stochastic-branching process model in which rates of speciation and extinction are constant between rate-shift events. We model three types of events: (1) instantaneous tree-wide shifts in speciation rate; (2) instantaneous tree-wide shifts in extinction rate, and; (3) instantaneous tree-wide mass-extinction events. Each of the events is described by a separate compound Poisson process (CPP) model, where the waiting times between each event are exponentially distributed with event-specific rate parameters. The magnitude of each event is drawn from an event-type specific prior distribution. Parameters of the model are then estimated using a reversible-jump Markov chain Monte Carlo (rjMCMC) algorithm. We demonstrate via simulation that this method has substantial power to detect the number of mass-extinction events, provides unbiased estimates of the timing of mass-extinction events, while exhibiting an appropriate (i.e., below 5%) false discovery rate even in the case of background diversification rate variation. Finally, we provide an empirical application of this approach to conifers, which reveals that this group has experienced two major episodes of mass extinction. This new approach?the CPP on Mass Extinction Times (CoMET) model?provides an effective tool for identifying mass-extinction events from molecular phylogenies, even when the history of those groups includes more prosaic temporal variation in diversification rate.

Incumbent replacement: evidence for long-term evolutionary progress

Paleobiology ◽  
1991 ◽  
Vol 17 (3) ◽  
pp. 202-213 ◽  
Author(s):  
Michael L. Rosenzweig ◽  
Robert D. McCord
Keyword(s):  
Mass Extinction ◽  
Extinction Rate ◽  
Trade Off ◽  
Evolutionary Progress ◽  
The North ◽  
Pure Chance ◽  
S Curve ◽  
Extinction Events ◽  
Mass Extinction Events

Evolutionary progress is a trend that relaxes trade-off rules. It begins with the evolution of a key adaptation. It continues with the spread of the key adaptation as the clade that contains it replaces some older clade that lacks it. Key adaptations are those that allow for improvement in at least one organismal function at a reduced fitness cost in other functions.Replacement almost certainly involves more than pure chance. It may not often involve competitive extinction. Instead, species from the new clade produce new species to replace already extinct species from the old clade. The key adaptation gives them a higher competitive speciation rate than old-clade sources of replacement. The process, termed incumbent replacement, proceeds at a rate limited by extinction rate. Thus, replacement often seems linked to mass extinction events.The incumbent-replacement hypothesis explains what we know about the replacement of straight-neck turtles (Amphichelydia) by those that can flex their necks and protect their heads in their shells. This replacement occurred four or five times in different biotic provinces. It happened as long ago as the Cretaceous in Eurasia, and as recently as the Pleistocene in mainland Australia. It was accomplished in Gondwanaland by turtles flexing their necks sideways (Pleurodira), and in the north by those flexing their necks into an S-curve (Cryptodira). As is typical of replacements, amphichelydian replacement took millions of years to accomplish wherever it occurred, and much of it in North America took place in a burst associated with and immediately subsequent to a mass extinction.

Taxonomic survivorship and morphologic complexity in Paleozoic bryozoan genera

Paleobiology ◽  
1978 ◽  
Vol 4 (4) ◽  
pp. 407-418 ◽  
Author(s):  
Robert L. Anstey
Keyword(s):  
Mass Extinction ◽  
Extinction Rate ◽  
Apparent Correlation ◽  
Complex Forms ◽  
Extinction Events ◽  
Mass Extinction Events

The shape of bryozoan taxonomic survivorship curves is strongly influenced both by grade of morphologic complexity and by mass extinction. Paleozoic bryozoan genera that are morphologically simple have linear taxonomic survivorship; morphologically intermediate taxa have slightly concave survivorship, and complex forms have very concave survivorship. Increasing morphologic complexity, and by inference, increasing specialization of adaptation appear to accompany a systematic departure from a stochastically constant extinction rate. However, the extinctions of the complex taxa are entirely concentrated during three mass extinction events, whereas the extinctions of the simple taxa are more uniformly distributed throughout the Paleozoic; the extinction pattern of the morphologically intermediate taxa is intermediate to those of the simple and complex groups. Exclusion of the genera affected by mass extinction increases the convexity of the survivorship curves, and reverses the apparent correlation of extinction rate with morphologic complexity. The macroevolutionary pattern of the complex genera resembles an r-strategy, whereas that of the simple taxa resembles a K-strategy.

scholarly journals Identifying the most surprising victims of mass extinction events: an example using Late Ordovician brachiopods

2017 ◽  
Vol 13 (9) ◽  
pp. 20170400 ◽  
Author(s):  
Seth Finnegan ◽  
Christian M. Ø. Rasmussen ◽  
David A. T. Harper
Keyword(s):  
Deep Water ◽  
Mass Extinction ◽  
Late Ordovician ◽  
Extinction Rate ◽  
Simple Method ◽  
Training Models ◽  
Extinction Event ◽  
Extinction Events ◽  
Mass Extinction Events

Mass extinction events are recognized by increases in extinction rate and magnitude and, often, by changes in the selectivity of extinction. When considering the selective fingerprint of a particular event, not all taxon extinctions are equally informative: some would be expected even under a ‘background’ selectivity regime, whereas others would not and thus require special explanation. When evaluating possible drivers for the extinction event, the latter group is of particular interest. Here, we introduce a simple method for identifying these most surprising victims of extinction events by training models on background extinction intervals and using these models to make per-taxon assessments of ‘expected’ risk during the extinction interval. As an example, we examine brachiopod genus extinctions during the Late Ordovician Mass Extinction and show that extinction of genera in the deep-water ‘ Foliomena fauna’ was particularly unexpected given preceding Late Ordovician extinction patterns.

Mass extinction patterns of marine invertebrate groups and some implications for a causal phenomenon

Paleobiology ◽  
1985 ◽  
Vol 11 (2) ◽  
pp. 227-233 ◽  
Author(s):  
Michael L. McKinney
Keyword(s):  
Late Cretaceous ◽  
Mass Extinction ◽  
Marine Invertebrate ◽  
Relative Increase ◽  
Late Triassic ◽  
Extinction Rate ◽  
Marine Fauna ◽  
Taxonomic Groups ◽  
Extinction Events ◽  
Mass Extinction Events

A nonparametric analysis of the extinction patterns of 10 major marine invertebrate groups at the five most profound mass extinction events leads to five observations: (1) At each event some taxonomic groups were affected much more than others. (2) There is little consistency among events in terms of which taxonomic groups were most or least affected; however, adaptive groupings do exhibit consistency: benthic, mobile organisms suffered significantly fewer extinctions than sessile suspension feeders, while the pelagic organisms apparently suffered the most. (3) There are no convincing patterns of interrelated extinctions among taxonomic groups. (4) No group exhibits a persistent tendency through time for a relative increase or decrease in their extinction rate at the events. (5) Some relationships are seen between the extinction patterns of three pairs of events; the Late Ordovician and Late Devonian events exhibit a significantly similar pattern (the same taxonomic groups suffered the most extinction in both cases) as do the Late Triassic and Late Cretaceous events. The Late Permian and Late Cretaceous events show a significantly inverse pattern (the most affected groups in the former were among the least affected in the latter). Upon examination, these observations, notably 1, 2, and 5, are consonant with current scenarios of the effects of catastrophic bolide impacts on marine fauna.

scholarly journals The primary divisions of life: a phylogenomic approach employing composition-heterogeneous methods

2009 ◽  
Vol 364 (1527) ◽  
pp. 2197-2207 ◽  
Author(s):  
Peter G. Foster ◽  
Cymon J. Cox ◽  
T. Martin Embley
Keyword(s):  
Sequence Data ◽  
Phylogenetic Signal ◽  
Amino Acid Sequences ◽  
Rate Variation ◽  
Molecular Sequence Data ◽  
Protein Coding ◽  
Molecular Sequence ◽  
Heterogeneous Models ◽  
Matrix Heterogeneity ◽  
Rna Genes

The three-domains tree, which depicts eukaryotes and archaebacteria as monophyletic sister groups, is the dominant model for early eukaryotic evolution. By contrast, the ‘eocyte hypothesis’, where eukaryotes are proposed to have originated from within the archaebacteria as sister to the Crenarchaeota (also called the eocytes), has been largely neglected in the literature. We have investigated support for these two competing hypotheses from molecular sequence data using methods that attempt to accommodate the across-site compositional heterogeneity and across-tree compositional and rate matrix heterogeneity that are manifest features of these data. When ribosomal RNA genes were analysed using standard methods that do not adequately model these kinds of heterogeneity, the three-domains tree was supported. However, this support was eroded or lost when composition-heterogeneous models were used, with concomitant increase in support for the eocyte tree for eukaryotic origins. Analysis of combined amino acid sequences from 41 protein-coding genes supported the eocyte tree, whether or not composition-heterogeneous models were used. The possible effects of substitutional saturation of our data were examined using simulation; these results suggested that saturation is delayed by among-site rate variation in the sequences, and that phylogenetic signal for ancient relationships is plausibly present in these data.

Mass extinctions alter extinction and origination dynamics with respect to body size

2021 ◽  
Vol 288 (1960) ◽  
Author(s):  
Pedro M. Monarrez ◽  
Noel A. Heim ◽  
Jonathan L. Payne
Keyword(s):  
Body Size ◽  
Mass Extinction ◽  
Evolutionary Biology ◽  
Marine Animal ◽  
Mass Extinctions ◽  
Extinction Selectivity ◽  
Extinction Events ◽  
Mass Extinction Events ◽  
Marine Biosphere

Whether mass extinctions and their associated recoveries represent an intensification of background extinction and origination dynamics versus a separate macroevolutionary regime remains a central debate in evolutionary biology. The previous focus has been on extinction, but origination dynamics may be equally or more important for long-term evolutionary outcomes. The evolution of animal body size is an ideal process to test for differences in macroevolutionary regimes, as body size is easily determined, comparable across distantly related taxa and scales with organismal traits. Here, we test for shifts in selectivity between background intervals and the ‘Big Five’ mass extinction events using capture–mark–recapture models. Our body-size data cover 10 203 fossil marine animal genera spanning 10 Linnaean classes with occurrences ranging from Early Ordovician to Late Pleistocene (485–1 Ma). Most classes exhibit differences in both origination and extinction selectivity between background intervals and mass extinctions, with the direction of selectivity varying among classes and overall exhibiting stronger selectivity during origination after mass extinction than extinction during the mass extinction. Thus, not only do mass extinction events shift the marine biosphere into a new macroevolutionary regime, the dynamics of recovery from mass extinction also appear to play an underappreciated role in shaping the biosphere in their aftermath.

scholarly journals Tip rates, phylogenies, and diversification: what are we estimating, and how good are the estimates?

2018 ◽  
Author(s):  
Pascal O. Title ◽  
Daniel L. Rabosky
Keyword(s):  
Diversification Rate ◽  
Rate Variation ◽  
Terminal Branch ◽  
List Type ◽  
Large Set ◽  
Extinction Rate ◽  
Diversification Rates ◽  
Speciation Rate ◽  
Model Based ◽  
Model Free

AbstractSpecies-specific diversification rates, or “tip rates”, can be computed quickly from phylogenies and are widely used to study diversification rate variation in relation to geography, ecology, and phenotypes. These tip rates provide a number of theoretical and practical advantages, such as the relaxation of assumptions of rate homogeneity in trait-dependent diversification studies. However, there is substantial confusion in the literature regarding whether these metrics estimate speciation or net diversification rates. Additionally, no study has yet compared the relative performance and accuracy of tip rate metrics across simulated diversification scenarios.We compared the statistical performance of three model-free rate metrics (inverse terminal branch lengths; node density metric; DR statistic) and a model-based approach (BAMM). We applied each method to a large set of simulated phylogenies that had been generated under different diversification processes; scenarios included multi-regime time-constant and diversity-dependent trees, as well as trees where the rate of speciation evolves under a diffusion process. We summarized performance in relation to the type of rate variation, the magnitude of rate heterogeneity and rate regime size. We also compared the ability of the metrics to estimate both speciation and net diversification rates.We show decisively that model-free tip rate metrics provide a better estimate of the rate of speciation than of net diversification. Error in net diversification rate estimates increases as a function of the relative extinction rate. In contrast, error in speciation rate estimates is low and relatively insensitive to extinction. Overall, and in particular when relative extinction was high, BAMM inferred the most accurate tip rates and exhibited lower error than non-model-based approaches. DR was highly correlated with true speciation rates but exhibited high error variance, and was the best metric for very small rate regimes.We found that, of the metrics tested, DR and BAMM are the most useful metrics for studying speciation rate dynamics and trait-dependent diversification. Although BAMM was more accurate than DR overall, the two approaches have complementary strengths. Because tip rate metrics are more reliable estimators of speciation rate, we recommend that empirical studies using these metrics exercise caution when drawing biological interpretations in any situation where the distinction between speciation and net diversification is important.

scholarly journals Nature's Design's: The Biology of Survival

2019 ◽  
Vol 301 ◽  
pp. 00023
Author(s):  
Pam Mantri ◽  
John Thomas
Keyword(s):  
Mass Extinction ◽  
Evolutionary Design ◽  
Bacterial Flagellum ◽  
Biotic Crisis ◽  
Rotary Engine ◽  
Systems Perspective ◽  
Complex Adaptive ◽  
Extinction Events ◽  
Mass Extinction Events

Life has existed on earth for at least 3.95 billion years. All along, the flame of life has been successfully passed on from generation to generation, and species to species across an immense temporal span. This includes at least five mass-extinction events that wiped out over 70% of all species in each such biotic crisis. Against such immense odds, life has learned to thrive despite repeat assaults. And the ingenuity embedded within natures designs has been an integral part of this inspiring story. For example, the ancient bacterial flagellum is powered by the Mot Complex which is part of a perfectly circular nanoscale rotary engine. It is obvious that nature came upon the wheel much before human arrival (i.e., at least as far back as 2.7 billion years). Many are the design lessons that may be gleaned from studying nature. This paper looks at the immense evolutionary design-laboratory that nature evolves its designs within, and frames it along side an Axiomatic/Complex-Adaptive/Stigmergic Systems perspective.

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