scholarly journals Why extinction estimates from extant phylogenies are so often zero

2021 ◽  
Author(s):  
Stilianos Louca ◽  
Matthew W. Pennell
Keyword(s):  
Maximum Likelihood ◽  
Fossil Record ◽  
Estimation Methods ◽  
Simple Explanation ◽  
Extinction Rate ◽  
Zero Inflation ◽  
Boundary Estimate ◽  
Extinction Rates ◽  
Phylogenetic Studies ◽  
Large Trees

AbstractTime-calibrated phylogenies comprising only extant lineages are widely used to estimate historical speciation and extinction rates. Such extinction rate estimates have long been controversial as many phylogenetic studies report zero extinction in many taxa, a finding in conflict with the fossil record. To date, the causes of this widely observed discrepancy remain unresolved. Here we provide a novel and simple explanation for these “zero-inflated” extinction rate estimates, based on the recent discovery that there exist many alternative “congruent” diversification scenarios that cannot possibly be distinguished on the sole basis of extant timetrees. Consequently, estimation methods tend to converge to some scenario congruent to (i.e., statistically indistinguishable from) the true diversification scenario, but not necessarily to the true diversification scenario itself. This congruent scenario may in principle exhibit negative extinction rates, a biologically meaningless but mathematically feasible situation, in which case estimators will tend to hit and stick to the boundary estimate of zero extinction. To test this explanation, we estimated extinction rates using maximum likelihood for a set of simulated trees and for 121 empirical trees, while either allowing or preventing negative extinction rates. We find that the existence of congruence classes and imposed bounds on extinction rates can explain the zero-inflation of previous extinction rate estimates, even for large trees (1000 tips) and in the absence of any detectable model violations. Not only do our results likely resolve a long-standing mystery in phylogenetics, they demonstrate that model congruencies can have severe consequences in practice.

Taxonomic survivorship curves and Van Valen's Law

Paleobiology ◽  
1975 ◽  
Vol 1 (1) ◽  
pp. 82-96 ◽  
Author(s):  
David M. Raup
Keyword(s):  
Fossil Record ◽  
Species Level ◽  
Extinction Rate ◽  
Survivorship Analysis ◽  
Survivorship Curve ◽  
Extinction Rates ◽  
Higher Taxa ◽  
Total Life ◽  
Adaptive Zone

As Van Valen has demonstrated, the taxonomic survivorship curve is a valuable means of investigating extinction rates in the fossil record. He suggested that within an adaptive zone, related taxa display stochastically constant and equal extinction rates. Such a condition is evidenced by straight survivorship curves for species and higher taxa. Van Valen's methods of survivorship analysis can be improved upon and several suggestions are presented. With proper manipulation of data, it is possible to pool the information from extinct and living taxa to produce a single survivorship curve and therefore a single estimate of extinction rate. If extinction rate is constant at the species level (producing a straight survivorship curve), higher taxa in the same group should be expected to have convex survivorship curves. The constancy of extinction rates (here termed Van Valen's Law) can and should be tested rigorously. Several methods are available, of which the Total Life method of Epstein is particularly effective.

scholarly journals Decline in extinction rates and scale invariance in the fossil record

Paleobiology ◽  
1999 ◽  
Vol 25 (4) ◽  
pp. 434-439 ◽  
Author(s):  
M. E. J. Newman ◽  
Gunther J. Eble
Keyword(s):  
Power Spectrum ◽  
Power Law ◽  
Fossil Record ◽  
Scale Invariance ◽  
Evolutionary Dynamics ◽  
Extinction Rate ◽  
Extinction Rates ◽  
Self Organized ◽  
Critical Theories ◽  
Extinction Events

We show that the decline in the extinction rate during the Phanerozoic can be accurately described by a logarithmic fit to the cumulative total extinction. This implies that extinction intensity is falling off approximately as the reciprocal of time. We demonstrate that this observation alone is sufficient to explain the existence of the proposed power-law forms in the distribution of the sizes of extinction events and in the power spectrum of Phanerozoic extinction, results that previously have been explained by appealing to self-organized critical theories of evolutionary dynamics.

scholarly journals Disjoint Tree Mergers for Large-Scale Maximum Likelihood Tree Estimation

Algorithms ◽  
2021 ◽  
Vol 14 (5) ◽  
pp. 148
Author(s):  
Minhyuk Park ◽  
Paul Zaharias ◽  
Tandy Warnow
Keyword(s):  
Maximum Likelihood ◽  
Gene Tree ◽  
Input Sequence ◽  
Species Tree ◽  
Estimation Methods ◽  
Biological Research ◽  
Species Trees ◽  
Basic Part ◽  
Large Trees ◽  
Tree Estimation

The estimation of phylogenetic trees for individual genes or multi-locus datasets is a basic part of considerable biological research. In order to enable large trees to be computed, Disjoint Tree Mergers (DTMs) have been developed; these methods operate by dividing the input sequence dataset into disjoint sets, constructing trees on each subset, and then combining the subset trees (using auxiliary information) into a tree on the full dataset. DTMs have been used to advantage for multi-locus species tree estimation, enabling highly accurate species trees at reduced computational effort, compared to leading species tree estimation methods. Here, we evaluate the feasibility of using DTMs to improve the scalability of maximum likelihood (ML) gene tree estimation to large numbers of input sequences. Our study shows distinct differences between the three selected ML codes—RAxML-NG, IQ-TREE 2, and FastTree 2—and shows that good DTM pipeline design can provide advantages over these ML codes on large datasets.

scholarly journals Current extinction rate in European freshwater gastropods greatly exceeds that of the late Cretaceous mass extinction

2021 ◽  
Vol 2 (1) ◽  
Author(s):  
Thomas A. Neubauer ◽  
Torsten Hauffe ◽  
Daniele Silvestro ◽  
Jens Schauer ◽  
Dietrich Kadolsky ◽  
...  
Keyword(s):  
Mass Extinction ◽  
Recovery Period ◽  
Freshwater Ecosystems ◽  
Extinction Rate ◽  
Freshwater Gastropods ◽  
Extinction Rates ◽  
Freshwater Biota ◽  
Order Of Magnitude ◽  
To Come ◽  
Mass Extinction Event

AbstractThe Cretaceous–Paleogene mass extinction event 66 million years ago eradicated three quarters of marine and terrestrial species globally. However, previous studies based on vertebrates suggest that freshwater biota were much less affected. Here we assemble a time series of European freshwater gastropod species occurrences and inferred extinction rates covering the past 200 million years. We find that extinction rates increased by more than one order of magnitude during the Cretaceous–Paleogene mass extinction, which resulted in the extinction of 92.5% of all species. The extinction phase lasted 5.4 million years and was followed by a recovery period of 6.9 million years. However, present extinction rates in European freshwater gastropods are three orders of magnitude higher than even these revised estimates for the Cretaceous–Paleogene mass extinction. Our results indicate that, unless substantial conservation effort is directed to freshwater ecosystems, the present extinction crisis will have a severe impact to freshwater biota for millions of years to come.

Properties and methods of estimation for a bivariate exponentiated Fréchet distribution

2020 ◽  
Vol 70 (5) ◽  
pp. 1211-1230
Author(s):  
Abdus Saboor ◽  
Hassan S. Bakouch ◽  
Fernando A. Moala ◽  
Sheraz Hussain
Keyword(s):  
Maximum Likelihood ◽  
Probability Density Function ◽  
Probability Density ◽  
Density Function ◽  
Superior Performance ◽  
Estimation Methods ◽  
Conditional Probability Density ◽  
Data Set ◽  
Fréchet Distribution ◽  
Frechet Distribution

AbstractIn this paper, a bivariate extension of exponentiated Fréchet distribution is introduced, namely a bivariate exponentiated Fréchet (BvEF) distribution whose marginals are univariate exponentiated Fréchet distribution. Several properties of the proposed distribution are discussed, such as the joint survival function, joint probability density function, marginal probability density function, conditional probability density function, moments, marginal and bivariate moment generating functions. Moreover, the proposed distribution is obtained by the Marshall-Olkin survival copula. Estimation of the parameters is investigated by the maximum likelihood with the observed information matrix. In addition to the maximum likelihood estimation method, we consider the Bayesian inference and least square estimation and compare these three methodologies for the BvEF. A simulation study is carried out to compare the performance of the estimators by the presented estimation methods. The proposed bivariate distribution with other related bivariate distributions are fitted to a real-life paired data set. It is shown that, the BvEF distribution has a superior performance among the compared distributions using several tests of goodness–of–fit.

scholarly journals Fossil biogeography: a new model to infer dispersal, extinction and sampling from palaeontological data

2016 ◽  
Vol 371 (1691) ◽  
pp. 20150225 ◽  
Author(s):  
Daniele Silvestro ◽  
Alexander Zizka ◽  
Christine D. Bacon ◽  
Borja Cascales-Miñana ◽  
Nicolas Salamin ◽  
...  
Keyword(s):  
North America ◽  
Fossil Record ◽  
Phylogenetic Trees ◽  
Phylogenetic Analyses ◽  
Historical Biogeography ◽  
Extinction Rates ◽  
Climatic Cooling ◽  
Fossil Data ◽  
Incomplete Sampling ◽  
Des Model

Methods in historical biogeography have revolutionized our ability to infer the evolution of ancestral geographical ranges from phylogenies of extant taxa, the rates of dispersals, and biotic connectivity among areas. However, extant taxa are likely to provide limited and potentially biased information about past biogeographic processes, due to extinction, asymmetrical dispersals and variable connectivity among areas. Fossil data hold considerable information about past distribution of lineages, but suffer from largely incomplete sampling. Here we present a new dispersal–extinction–sampling (DES) model, which estimates biogeographic parameters using fossil occurrences instead of phylogenetic trees. The model estimates dispersal and extinction rates while explicitly accounting for the incompleteness of the fossil record. Rates can vary between areas and through time, thus providing the opportunity to assess complex scenarios of biogeographic evolution. We implement the DES model in a Bayesian framework and demonstrate through simulations that it can accurately infer all the relevant parameters. We demonstrate the use of our model by analysing the Cenozoic fossil record of land plants and inferring dispersal and extinction rates across Eurasia and North America. Our results show that biogeographic range evolution is not a time-homogeneous process, as assumed in most phylogenetic analyses, but varies through time and between areas. In our empirical assessment, this is shown by the striking predominance of plant dispersals from Eurasia into North America during the Eocene climatic cooling, followed by a shift in the opposite direction, and finally, a balance in biotic interchange since the middle Miocene. We conclude by discussing the potential of fossil-based analyses to test biogeographic hypotheses and improve phylogenetic methods in historical biogeography.

scholarly journals New Lindley Half Cauchy Distribution: Theory and Applications

2020 ◽  
Vol 9 (4) ◽  
pp. 1-7
Keyword(s):  
Maximum Likelihood ◽  
Real Data ◽  
Cauchy Distribution ◽  
Least Square ◽  
Cumulative Distribution ◽  
Likelihood Method ◽  
Estimation Methods ◽  
Model Parameters ◽  
Data Set ◽  
Von Mises

In this paper, we have defined a new two-parameter new Lindley half Cauchy (NLHC) distribution using Lindley-G family of distribution which accommodates increasing, decreasing and a variety of monotone failure rates. The statistical properties of the proposed distribution such as probability density function, cumulative distribution function, quantile, the measure of skewness and kurtosis are presented. We have briefly described the three well-known estimation methods namely maximum likelihood estimators (MLE), least-square (LSE) and Cramer-Von-Mises (CVM) methods. All the computations are performed in R software. By using the maximum likelihood method, we have constructed the asymptotic confidence interval for the model parameters. We verify empirically the potentiality of the new distribution in modeling a real data set.

Fossil preservation and the stratigraphic ranges of taxa

Paleobiology ◽  
1996 ◽  
Vol 22 (2) ◽  
pp. 121-140 ◽  
Author(s):  
Mike Foote ◽  
David M. Raup
Keyword(s):  
Fossil Record ◽  
Mammalian Species ◽  
Evolutionary Rates ◽  
Extinction Rate ◽  
Mammal Species ◽  
Original Distribution ◽  
Lower Ordovician ◽  
Stratigraphic Ranges ◽  
Fossil Preservation ◽  
Rule Out

The incompleteness of the fossil record hinders the inference of evolutionary rates and patterns. Here, we derive relationships among true taxonomic durations, preservation probability, and observed taxonomic ranges. We use these relationships to estimate original distributions of taxonomic durations, preservation probability, and completeness (proportion of taxa preserved), given only the observed ranges. No data on occurrences within the ranges of taxa are required. When preservation is random and the original distribution of durations is exponential, the inference of durations, preservability, and completeness is exact. However, reasonable approximations are possible given non-exponential duration distributions and temporal and taxonomic variation in preservability. Thus, the approaches we describe have great potential in studies of taphonomy, evolutionary rates and patterns, and genealogy.Analyses of Upper Cambrian-Lower Ordovician trilobite species, Paleozoic crinoid genera, Jurassic bivalve species, and Cenozoic mammal species yield the following results: (1) The preservation probability inferred from stratigraphic ranges alone agrees with that inferred from the analysis of stratigraphic gaps when data on the latter are available. (2) Whereas median durations based on simple tabulations of observed ranges are biased by stratigraphic resolution, our estimates of median duration, extinction rate, and completeness are not biased. (3) The shorter geologic ranges of mammalian species relative to those of bivalves cannot be attributed to a difference in preservation potential. However, we cannot rule out the contribution of taxonomic practice to this difference. (4) In the groups studied, completeness (proportion of species [trilobites, bivalves, mammals] or genera [crinoids] preserved) ranges from 60% to 90%. The higher estimates of completeness at smaller geographic scales support previous suggestions that the incompleteness of the fossil record reflects loss of fossiliferous rock more than failure of species to enter the fossil record in the first place.

Jaya algorithm in estimation of P[X > Y] for two parameter Weibull distribution

2022 ◽  
Vol 7 (2) ◽  
pp. 2820-2839
Author(s):  
Saurabh L. Raikar ◽  
◽  
Dr. Rajesh S. Prabhu Gaonkar ◽  
Keyword(s):  
Maximum Likelihood ◽  
Maximum Likelihood Estimation ◽  
Weibull Distribution ◽  
Least Squares ◽  
Weighted Least Squares ◽  
Real Life ◽  
Likelihood Estimation ◽  
Estimation Methods ◽  
Jaya Algorithm ◽  
Two Parameter

<abstract> <p>Jaya algorithm is a highly effective recent metaheuristic technique. This article presents a simple, precise, and faster method to estimate stress strength reliability for a two-parameter, Weibull distribution with common scale parameters but different shape parameters. The three most widely used estimation methods, namely the maximum likelihood estimation, least squares, and weighted least squares have been used, and their comparative analysis in estimating reliability has been presented. The simulation studies are carried out with different parameters and sample sizes to validate the proposed methodology. The technique is also applied to real-life data to demonstrate its implementation. The results show that the proposed methodology's reliability estimates are close to the actual values and proceeds closer as the sample size increases for all estimation methods. Jaya algorithm with maximum likelihood estimation outperforms the other methods regarding the bias and mean squared error.</p> </abstract>

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