Estimating the number of pulses in a mass extinction

Paleobiology ◽  
2018 ◽  
Vol 44 (2) ◽  
pp. 199-218 ◽  
Author(s):  
Steve C. Wang ◽  
Ling Zhong
Keyword(s):  
Mass Extinction ◽  
Fossil Record ◽  
Nearest Neighbor ◽  
Hypothesis Test ◽  
Information Criterion ◽  
Data Set ◽  
Recovery Potential ◽  
Step Algorithm ◽  
Extinction Events ◽  
Fossil Preservation

AbstractThe Signor-Lipps effect states that even a sudden mass extinction will invariably appear gradual in the fossil record, due to incomplete fossil preservation. Most previous work on the Signor–Lipps effect has focused on testing whether taxa in a mass extinction went extinct simultaneously or gradually. However, many authors have proposed scenarios in which taxa went extinct in distinct pulses. Little methodology has been developed for quantifying characteristics of such pulsed extinction events. Here we introduce a method for estimating the number of pulses in a mass extinction, based on the positions of fossil occurrences in a stratigraphic section. Rather than using a hypothesis test and assuming simultaneous extinction as the default, we reframe the question by asking what number of pulses best explains the observed fossil record.Using a two-step algorithm, we are able to estimate not just the number of extinction pulses but also a confidence level or posterior probability for each possible number of pulses. In the first step, we find the maximum likelihood estimate for each possible number of pulses. In the second step, we calculate the Akaike information criterion and Bayesian information criterion weights for each possible number of pulses, and then apply ak-nearest neighbor classifier to these weights. This method gives us a vector of confidence levels for the number of extinction pulses—for instance, we might be 80% confident that there was a single extinction pulse, 15% confident that there were two pulses, and 5% confident that there were three pulses. Equivalently, we can state that we are 95% confident that the number of extinction pulses is one or two. Using simulation studies, we show that the method performs well in a variety of situations, although it has difficulty in the case of decreasing fossil recovery potential, and it is most effective for small numbers of pulses unless the sample size is large. We demonstrate the method using a data set of Late Cretaceous ammonites.

scholarly journals Completeness of the eutherian mammal fossil record and implications for reconstructing mammal evolution through the Cretaceous/Paleogene mass extinction

Paleobiology ◽  
2017 ◽  
Vol 43 (4) ◽  
pp. 521-536 ◽  
Author(s):  
Thomas W. Davies ◽  
Mark A. Bell ◽  
Anjali Goswami ◽  
Thomas J. D. Halliday
Keyword(s):  
Mass Extinction ◽  
Fossil Record ◽  
Information Criterion ◽  
Molecular Data ◽  
Tectonic Activity ◽  
Eutherian Mammal ◽  
Geological Time ◽  
Data Set ◽  
Significant Difference ◽  
The Difference

AbstractThere is a well-established discrepancy between paleontological and molecular data regarding the timing of the origin and diversification of placental mammals. Molecular estimates place interordinal diversification dates in the Cretaceous, while no unambiguous crown placental fossils have been found prior to the end-Cretaceous mass extinction. Here, the completeness of the eutherian fossil record through geological time is evaluated to assess the suggestion that a poor fossil record is largely responsible for the difference in estimates of placental origins. The completeness of fossil specimens was measured using the character completeness metric, which quantifies the completeness of fossil taxa as the percentage of phylogenetic characters available to be scored for any given taxon. Our data set comprised 33 published cladistic matrices representing 445 genera, of which 333 were coded at the species level.There was no significant difference in eutherian completeness across the Cretaceous/Paleogene (K/Pg) boundary. This suggests that the lack of placental mammal fossils in the Cretaceous is not due to a poor fossil record but more likely represents a genuine absence of placental mammals in the Cretaceous. This result supports the “explosive model” of early placental evolution, whereby placental mammals originated around the time of the K/Pg boundary and diversified soon after.No correlation was found between the completeness pattern observed in this study and those of previous completeness studies on birds and sauropodomorph dinosaurs, suggesting that different factors affect the preservation of these groups. No correlations were found with various isotope proxy measures, but Akaike information criterion analysis found that eutherian character completeness metric scores were best explained by models involving the marine-carbonate strontium-isotope ratios (87Sr/86Sr), suggesting that tectonic activity might play a role in controlling the completeness of the eutherian fossil record.

scholarly journals Confidence intervals for pulsed mass extinction events

Paleobiology ◽  
2007 ◽  
Vol 33 (2) ◽  
pp. 324-336 ◽  
Author(s):  
Steve C. Wang ◽  
Philip J. Everson
Keyword(s):  
Confidence Intervals ◽  
Mass Extinction ◽  
Fossil Record ◽  
Marine Invertebrates ◽  
Ratio Test ◽  
Mass Extinctions ◽  
Data Set ◽  
Triassic Boundary ◽  
Multiple Pulses ◽  
Extinction Events

Many authors have proposed scenarios for mass extinctions that consist of multiple pulses or stages, but little work has been done on accounting for the Signor-Lipps effect in such extinction scenarios. Here we introduce a method for computing confidence intervals for the time or stratigraphic distance separating two extinction pulses in a pulsed extinction event, taking into account the incompleteness of the fossil record. We base our method on a flexible likelihood ratio test framework that is able to test whether the fossil record is consistent with any extinction scenario, whether simultaneous, pulsed, or otherwise. As an illustration, we apply our method to a data set on marine invertebrates from the Permo-Triassic boundary of Meishan, China. Using this data set, we show that the fossil record of ostracodes and that of brachiopods are each consistent with simultaneous extinction, and that these two extinction pulses are separated by 720,000 to 1.2 million years with 95% confidence. With appropriate data, our method could also be applied in other situations, such as tests of origination patterns, coordinated stasis, and recovery after a mass extinction.

The biology of mass extinction: a palaeontological view

1989 ◽  
Vol 325 (1228) ◽  
pp. 357-368 ◽  
Keyword(s):  
Mass Extinction ◽  
Large Scale ◽  
Individual Species ◽  
Ecological Groups ◽  
Mass Extinctions ◽  
Geological Time ◽  
Evolutionary Patterns ◽  
Data Set ◽  
High Species Richness ◽  
Extinction Events

Extinctions are not biologically random: certain taxa or functional/ecological groups are more extinction-prone than others. Analysis of molluscan survivorship patterns for the end-Cretaceous mass extinctions suggests that some traits that tend to confer extinction resistance during times of normal (‘background’) levels of extinction are ineffectual during mass extinction. For genera, high species-richness and possession of widespread individual species imparted extinction-resistance during background times but not during the mass extinction, when overall distribution of the genus was an important factor. Reanalysis of Hoffman’s (1986) data ( Neues Jb. Geol. Palaont. Abh. 172, 219) on European bivalves, and preliminary analysis of a new northern European data set, reveals a similar change in survivorship rules, as do data scattered among other taxa and extinction events. Thus taxa and adaptations can be lost not because they were poorly adapted by the standards of the background processes that constitute the bulk of geological time, but because they lacked - or were not linked to - the organismic, species-level or clade-level traits favoured under mass-extinction conditions. Mass extinctions can break the hegemony of species-rich, well-adapted clades and thereby permit radiation of taxa that had previously been minor faunal elements; no net increase in the adaptation of the biota need ensue. Although some large-scale evolutionary trends transcend mass extinctions, post-extinction evolutionary pathways are often channelled in directions not predictable from evolutionary patterns during background times.

scholarly journals Stratigraphic signatures of mass extinctions: ecological and sedimentary determinants

2018 ◽  
Vol 285 (1886) ◽  
pp. 20181191 ◽  
Author(s):  
Rafał Nawrot ◽  
Daniele Scarponi ◽  
Michele Azzarone ◽  
Troy A. Dexter ◽  
Kristopher M. Kusnerik ◽  
...  
Keyword(s):  
Mass Extinction ◽  
Local Community ◽  
Empirical Studies ◽  
Mass Extinctions ◽  
Sea Level Changes ◽  
Sequence Stratigraphic ◽  
Recovery Potential ◽  
Mollusc Species ◽  
Stratigraphic Ranges ◽  
Extinction Events

Stratigraphic patterns of last occurrences (LOs) of fossil taxa potentially fingerprint mass extinctions and delineate rates and geometries of those events. Although empirical studies of mass extinctions recognize that random sampling causes LOs to occur earlier than the time of extinction (Signor–Lipps effect), sequence stratigraphic controls on the position of LOs are rarely considered. By tracing stratigraphic ranges of extant mollusc species preserved in the Holocene succession of the Po coastal plain (Italy), we demonstrated that, if mass extinction took place today, complex but entirely false extinction patterns would be recorded regionally due to shifts in local community composition and non-random variation in the abundance of skeletal remains, both controlled by relative sea-level changes. Consequently, rather than following an apparent gradual pattern expected from the Signor–Lipps effect, LOs concentrated within intervals of stratigraphic condensation and strong facies shifts mimicking sudden extinction pulses. Methods assuming uniform recovery potential of fossils falsely supported stepwise extinction patterns among studied species and systematically underestimated their stratigraphic ranges. Such effects of stratigraphic architecture, co-produced by ecological, sedimentary and taphonomic processes, can easily confound interpretations of the timing, duration and selectivity of mass extinction events. Our results highlight the necessity of accounting for palaeoenvironmental and sequence stratigraphic context when inferring extinction dynamics from the fossil record.

Abundance and extinction in Ordovician–Silurian brachiopods, Cincinnati Arch, Ohio and Kentucky

Paleobiology ◽  
2012 ◽  
Vol 38 (2) ◽  
pp. 278-291 ◽  
Author(s):  
Andrew Zaffos ◽  
Steven M. Holland
Keyword(s):  
Spatial Scale ◽  
Mass Extinction ◽  
Fossil Record ◽  
Late Ordovician ◽  
Complex Relationship ◽  
Third Order ◽  
Evolutionary Advantage ◽  
Basic Hypothesis ◽  
Extinction Events ◽  
The Relationship

A basic hypothesis in extinction theory predicts that more abundant taxa have an evolutionary advantage over less abundant taxa, which should manifest as increased survivorship during major extinction events and longer fossil-record durations. Despite this, various paleontologic studies have found conflicting patterns, indicating a more complex relationship between abundance and extinction in the geologic past. This study tests the relationship between abundance and extinction among brachiopod genera within seven third-order depositional sequences spanning the Late Ordovician to Early Silurian (Katian–Aeronian) of the Cincinnati Arch.Contrary to predictions, abundance is not positively correlated with duration in this study. Abundance and duration range from strongly negatively correlated to uncorrelated depending on the spatial scale of analysis and the geologic intervals included, but correlations never indicate that abundance is an evolutionary advantage. In contrast, abundance was an advantageous trait prior to the Ordovician/Silurian extinction, and brachiopods with higher abundances were more likely to survive the event than less abundant brachiopods. While this result is in keeping with common models of extinction, it has not been observed previously at a mass extinction boundary. This may be further evidence that the Ordovician/Silurian extinction was not accompanied by a shift in the macroevolutionary selectivity regime.

Mass extinction events and the plant fossil record

2007 ◽  
Vol 22 (10) ◽  
pp. 548-557 ◽  
Author(s):  
Jennifer C. McElwain ◽  
Surangi W. Punyasena
Keyword(s):  
Mass Extinction ◽  
Fossil Record ◽  
Plant Fossil ◽  
Extinction Events ◽  
Mass Extinction Events

Evidence for extinction selectivity throughout the marine invertebrate fossil record

Paleobiology ◽  
2009 ◽  
Vol 35 (4) ◽  
pp. 553-564 ◽  
Author(s):  
G. Alex Janevski ◽  
Tomasz K. Baumiller
Keyword(s):  
Species Richness ◽  
Mass Extinction ◽  
Fossil Record ◽  
Marine Invertebrate ◽  
Species Level ◽  
Geologic History ◽  
Extinction Selectivity ◽  
Extinction Events ◽  
Open Question ◽  
Mass Extinction Events

The fossil record has been used to show that in some geologic intervals certain traits of taxa may increase their survivability, and therefore that the risk of extinction is not randomly distributed among taxa. It has also been suggested that traits that buffer against extinction in background times do not confer the same resistance during mass extinction events. An open question is whether at any time in geologic history extinction probabilities were randomly distributed among taxa. Here we use a method for detecting random extinction to demonstrate that during both background and mass extinction times, extinction of marine invertebrate genera has been nonrandom with respect to species richness categories of genera. A possible cause for this nonrandom extinction is selective clustering of extinctions in genera consisting of species which possess extinction-biasing traits. Other potential causes considered here include geographic selectivity, increased extinction susceptibility for species in species-rich genera, or biases related to taxonomic practice and/or sampling heterogeneity. An important theoretical result is that extinction selectivity at the species level cannot be smoothly extrapolated upward to genera; the appearance of random genus extinction with respect to species richness of genera results when extinction has been highly selective at the species level.

Infaunal response during the end-Permian mass extinction

2020 ◽  
Vol 133 (1-2) ◽  
pp. 91-99 ◽  
Author(s):  
Mao Luo ◽  
Luis A. Buatois ◽  
G.R. Shi ◽  
Zhong-Qiang Chen
Keyword(s):  
Mixed Layer ◽  
Mass Extinction ◽  
Fossil Record ◽  
Sea Water ◽  
The Body ◽  
Trace Fossil ◽  
Late Permian ◽  
Data Set ◽  
Permian Mass Extinction ◽  
Body Fossil

Abstract The end-Permian mass extinction (EPME) profoundly shaped shallow marine ecosystems. Although much has been learned about this event based on the body-fossil record, the global infaunal response to the EPME, as represented by ichnofossils, is much less understood. Here we analyze secular changes in ichnodiversity and ichnodisparity from the late Permian to the Middle Triassic based on a global trace-fossil data set. Results show that, in contrast to the body-fossil record, late Permian global ichnodiversity and ichnodisparity maintained their level until the Griesbachian, followed by a sharp loss in the Dienerian. Notably, the Griesbachian shows an unusual dominance of shallower tiers. The discrepancy between the body- and trace-fossil record is interpreted to be the result of the resurgence of widespread microbial matgrounds in the Griesbachian that aided the preservation of surface, semi-infaunal, and shallow-tier ichnofossils. Our study shows that the EPME strongly affected the sediment mixed layer, allowing the preservation of shallower tier trace fossils. The disappearance of the mixed layer in the earliest Triassic may have enhanced pyrite burial in sediments and inhibited its further re-oxidation, therefore impacting sea water sulfate concentrations.

Machine Learning Verdict of EEG Signals in Brain Computer Interface

2018 ◽  
pp. 429-441
Author(s):  
M. Jeyanthi ◽  
C. Velayutham
Keyword(s):  
Nearest Neighbor ◽  
Technology Development ◽  
Vital Role ◽  
Svm Classifier ◽  
K Nearest Neighbor ◽  
Data Mining Technique ◽  
Data Set ◽  
Eeg Data ◽  
Irrelevant Attributes

In Science and Technology Development BCI plays a vital role in the field of Research. Classification is a data mining technique used to predict group membership for data instances. Analyses of BCI data are challenging because feature extraction and classification of these data are more difficult as compared with those applied to raw data. In this paper, We extracted features using statistical Haralick features from the raw EEG data . Then the features are Normalized, Binning is used to improve the accuracy of the predictive models by reducing noise and eliminate some irrelevant attributes and then the classification is performed using different classification techniques such as Naïve Bayes, k-nearest neighbor classifier, SVM classifier using BCI dataset. Finally we propose the SVM classification algorithm for the BCI data set.

SEMIPARAMETRIC CLUSTERING METHOD FOR MICROARRAY DATA ANALYSIS

2008 ◽  
Vol 06 (02) ◽  
pp. 261-282 ◽  
Author(s):  
AO YUAN ◽  
WENQING HE
Keyword(s):  
Data Analysis ◽  
Microarray Data ◽  
Mixture Distribution ◽  
Information Criterion ◽  
Optimal Number ◽  
Microarray Data Analysis ◽  
Parametric Methods ◽  
Clustering Methods ◽  
Microarray Gene Expression ◽  
Data Set

Clustering is a major tool for microarray gene expression data analysis. The existing clustering methods fall mainly into two categories: parametric and nonparametric. The parametric methods generally assume a mixture of parametric subdistributions. When the mixture distribution approximately fits the true data generating mechanism, the parametric methods perform well, but not so when there is nonnegligible deviation between them. On the other hand, the nonparametric methods, which usually do not make distributional assumptions, are robust but pay the price for efficiency loss. In an attempt to utilize the known mixture form to increase efficiency, and to free assumptions about the unknown subdistributions to enhance robustness, we propose a semiparametric method for clustering. The proposed approach possesses the form of parametric mixture, with no assumptions to the subdistributions. The subdistributions are estimated nonparametrically, with constraints just being imposed on the modes. An expectation-maximization (EM) algorithm along with a classification step is invoked to cluster the data, and a modified Bayesian information criterion (BIC) is employed to guide the determination of the optimal number of clusters. Simulation studies are conducted to assess the performance and the robustness of the proposed method. The results show that the proposed method yields reasonable partition of the data. As an illustration, the proposed method is applied to a real microarray data set to cluster genes.

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