scholarly journals Assessing the impact of incomplete species sampling on estimates of speciation and extinction rates

Paleobiology ◽  
2020 ◽  
Vol 46 (2) ◽  
pp. 137-157 ◽  
Author(s):  
Rachel C. M. Warnock ◽  
Tracy A. Heath ◽  
Tanja Stadler
Keyword(s):  
Alternative Methods ◽  
Range Data ◽  
Phylogenetic Structure ◽  
Diversification Rates ◽  
Extinction Rates ◽  
Living Species ◽  
Stratigraphic Ranges ◽  
Fossil Records ◽  
Fossil Data ◽  
The Impact

AbstractEstimating speciation and extinction rates is essential for understanding past and present biodiversity, but is challenging given the incompleteness of the rock and fossil records. Interest in this topic has led to a divergent suite of independent methods—paleontological estimates based on sampled stratigraphic ranges and phylogenetic estimates based on the observed branching times in a given phylogeny of living species. The fossilized birth–death (FBD) process is a model that explicitly recognizes that the branching events in a phylogenetic tree and sampled fossils were generated by the same underlying diversification process. A crucial advantage of this model is that it incorporates the possibility that some species may never be sampled. Here, we present an FBD model that estimates tree-wide diversification rates from stratigraphic range data when the underlying phylogeny of the fossil taxa may be unknown. The model can be applied when only occurrence data for taxonomically identified fossils are available, but still accounts for the incomplete phylogenetic structure of the data. We tested this new model using simulations and focused on how inferences are impacted by incomplete fossil recovery. We compared our approach with a phylogenetic model that does not incorporate incomplete species sampling and to three fossil-based alternatives for estimating diversification rates, including the widely implemented boundary-crosser and three-timer methods. The results of our simulations demonstrate that estimates under the FBD model are robust and more accurate than the alternative methods, particularly when fossil data are sparse, as the FBD model incorporates incomplete species sampling explicitly.

scholarly journals Fossils Do Not Substantially Improve, and May Even Harm, Estimates of Diversification Rate Heterogeneity

2021 ◽  
Author(s):  
Jeremy M Beaulieu ◽  
Brian C O'Meara
Keyword(s):  
Diversification Rate ◽  
Turnover Rates ◽  
Rate Heterogeneity ◽  
Diversification Rates ◽  
Stratigraphic Ranges ◽  
Fossil Data ◽  
The Impact ◽  
Prevailing View ◽  
Birth Death

There is a prevailing view that the inclusion of fossil data could remedy identifiability issues related to models of diversification, by drastically reducing the number of congruent models. The fossilized birth-death (FBD) model is an appealing way of directly incorporating fossil information when estimating diversification rates. Here we explore the benefits of including fossils by implementing and then testing two-types of FBD models in more complex likelihood-based models that assume multiple rate classes across the tree. We also assess the impact of severely undersampling, and even not including fossils that represent samples of lineages that also had sampled descendants (i.e., k-type fossils), as well as converting a fossil set to represent stratigraphic ranges. Under various simulation scenarios, including a scenario that exists far outside the set of models we evaluated, including fossils rarely outperforms analyses that exclude them altogether. At best, the inclusion of fossils improves precision but does not influence bias. We also found that severely undercounting the number of k-type fossils produces highly inflated rates of turnover and extinction fraction. Similarly, we found that converting the fossil set to stratigraphic ranges results in turnover rates and extinction fraction estimates that are generally underestimated. While fossils remain essential for understanding diversification through time, in the specific case of understanding diversification given an existing, largely modern tree, they are not especially beneficial.

scholarly journals Detecting diversification rates in relation to preservation and tectonic history from simulated fossil records

Paleobiology ◽  
2018 ◽  
Vol 44 (1) ◽  
pp. 1-24 ◽  
Author(s):  
Tara M. Smiley
Keyword(s):  
Fossil Record ◽  
Strong Relationship ◽  
Tectonic Activity ◽  
Diversification Rates ◽  
Topographic Complexity ◽  
Extinction Rates ◽  
The North ◽  
Rock Record ◽  
Per Capita ◽  
Fossil Records

AbstractFor mammals today, mountains are diverse ecosystems globally, yet the strong relationship between species richness and topographic complexity is not a persistent feature of the fossil record. Based on fossil-occurrence data, diversity and diversification rates in the intermontane western North America varied through time, increasing significantly during an interval of global warming and regional intensification of tectonic activity from 18 to 14 Ma. However, our ability to infer origination and extinction rates reliably from the fossil record is affected by variation in preservation history. To investigate the influence of preservation on estimates of diversification rates, I simulated fossil records under four alternative diversification hypotheses and six preservation scenarios. Diversification hypotheses included tectonically controlled speciation pulses, while preservation scenarios were based on common trends (e.g., increasing rock record toward the present) or derived from fossil occurrences and the continental rock record. For each scenario, I estimated origination, extinction, and diversification rates using three standard methods—per capita, three-timer, and capture–mark–recapture (CMR) metrics—and evaluated the ability of the simulated fossil records to accurately recover the underlying diversification dynamics. Despite variable and low preservation probabilities, simulated fossil records retained the signal of true rates in several of the scenarios. The three metrics did not exhibit similar behavior under each preservation scenario: while three-timer and CMR metrics produced more accurate rate estimates, per capita rates tended to better reproduce true shifts in origination rates. All metrics suffered from spurious peaks in origination and extinction rates when highly volatile preservation impacted the simulated record. Results from these simulations indicate that elevated diversification rates in relation to tectonic activity during the middle Miocene are likely to be evident in the fossil record, even if preservation in the North American fossil record was variable. Input from the past is necessary to evaluate the ultimate mechanisms underlying speciation and extinction dynamics.

Variation between groups in evolutionary rates: a statistical test of significance

Paleobiology ◽  
1980 ◽  
Vol 6 (1) ◽  
pp. 9-23 ◽  
Author(s):  
David M. Raup ◽  
Larry G. Marshall
Keyword(s):  
Statistical Significance ◽  
Range Data ◽  
South American ◽  
High Turnover ◽  
Chi Square ◽  
Data Set ◽  
Extinction Rates ◽  
Test Of Significance ◽  
Stratigraphic Ranges ◽  
Taxonomic Groups

The statistical significance of differences in evolutionary rate between major taxonomic groups is evaluated using conventional chi-square techniques on stratigraphic range data. Romer's (1966) compilation of stratigraphic ranges of fossil mammals is used to determine whether orders differ significantly from each other in generic origination and extinction rates. The evolutionary histories of 2180 genera (primarily Cenozoic in age) are analyzed. Chi-square testing shows that significantly high or low (P ≥ 0.99) extinction or origination occurs in 15% of the testable cases. Significantly high or low evolutionary turnover in a taxon (orders in this case) we term taxotely. Significantly high turnover rate is equivalent to Simpson's tachytely and significantly low turnover is equivalent to his bradytely.In the mammal data set, taxotely is largely attributable to the influence of South American endemics. Some of the effect is interpreted as an artifact of biases in the fossil record (or its study) and some is attributed to real biological aspects of mammalian evolution.

Fair Sampling of Taxonomic Richness and Unbiased Estimation of Origination and Extinction Rates

2010 ◽  
Vol 16 ◽  
pp. 55-80 ◽  
Author(s):  
John Alroy
Keyword(s):  
Statistical Estimation ◽  
Alternative Methods ◽  
Estimation Methods ◽  
Unbiased Estimation ◽  
Fixed Target ◽  
Data Set ◽  
Extinction Rates ◽  
True Diversity ◽  
Fossil Data ◽  
Diversity Estimates

Paleobiologists are reaching a consensus that biases in diversity curves, origination rates, and extinction rates need to be removed using statistical estimation methods. Diversity estimates are biased both by methods of counting and by variation in the amount of fossil data. Traditional counts are essentially tallies of age ranges. Because these counts are distorted by interrelated factors such as the Pull of the Recent and the Signor-Lipps effect, counts of taxa actually sampled within intervals should be used instead. Sampling intensity biases can be addressed with randomized subsampling of data records such as individual taxonomic occurrences or entire fossil collections. Fair subsampling would yield taxon counts that track changes in the species pool size, i.e., the diversity of all taxa that could ever be sampled. Most of the literature has overlooked this point, having instead focused on making sample sizes uniform through methods such as rarefaction. These methods flatten the data, undersampling when true diversity is high. A good solution to this problem involves the concept of frequency distribution coverage: a taxon's underlying frequency is said to be “covered” when it is represented by at least one fossil in a data set. A fair subsample, but not a uniform one, can be created by drawing collections until estimated coverage reaches a fixed target (i.e., until a “shareholder quorum” is attained). Origination and extinction rates present other challenges. For many years they were thought of in terms of simple counts or ratios, but they are now treated as exponential decay coefficients of the kind featuring in simple birth-death models. Unfortunately, these instantaneous rates also suffer from counting method biases (e.g., the Pull of the Recent). Such biases can be removed by only examining taxa sampled twice consecutively, three times consecutively, or in the first and third of three intervals but not the second (i.e., two timers, three timers, and part timers). Two similar equations involving these counts can be used. Alternative methods of estimating diversity and turnover through extrapolation share some of the advantages of quorum subsampling and two-timer family equations, but it remains to be shown whether they produce precise and accurate estimates when applied to fossil data.

Testing for variation in taxonomic extinction probabilities: a suggested methodology and some results

Paleobiology ◽  
1984 ◽  
Vol 10 (3) ◽  
pp. 328-337 ◽  
Author(s):  
Michael J. Conroy ◽  
James D. Nichols
Keyword(s):  
Stochastic Models ◽  
Evolutionary Biology ◽  
Range Data ◽  
Geologic Time ◽  
Extinction Rates ◽  
Extinction Probabilities ◽  
Sources Of Variation ◽  
Time Periods ◽  
Fossil Data ◽  
Stratigraphic Range

Several important questions in evolutionary biology and paleobiology involve sources of variation in extinction rates. In all cases of which we are aware, extinction rates have been estimated from data in which the probability that an observation (e.g., a fossil taxon) will occur is related both to extinction rates and to what we term encounter probabilities. Any statistical method for analyzing fossil data should at a minimum permit separate inferences on these two components. We develop a method for estimating taxonomic extinction rates from stratigraphic range data and for testing hypotheses about variability in these rates. We use this method to estimate extinction rates and to test the hypothesis of constant extinction rates for several sets of stratigraphic range data. The results of our tests support the hypothesis that extinction rates varied over the geologic time periods examined. We also present a test that can be used to identify periods of high or low extinction probabilities and provide an example using Phanerozoic invertebrate data. Extinction rates should be analyzed using stochastic models, in which it is recognized that stratigraphic samples are random variates and that sampling is imperfect.

Evaluation of Hydraulic Fracturing Models and Their Limitations to Predict No-Drill Zones for Horizontal Directional Drilling

2018 ◽  
Author(s):  
Saeed Delara ◽  
Kendra MacKay
Keyword(s):  
Hydraulic Fracturing ◽  
Safety Factor ◽  
Standard Procedure ◽  
Accurate Determination ◽  
Strength Properties ◽  
Analytical Models ◽  
Alternative Methods ◽  
Directional Drilling ◽  
Horizontal Directional Drilling ◽  
The Impact

Horizontal directional drilling (HDD) has become the preferred method for trenchless pipeline installations. Drilling pressures must be limited and a “no-drill zone” determined to avoid exceeding the strength of surrounding soil and rock. The currently accepted industry method of calculating hydraulic fracturing limiting pressure with application of an arbitrary safety factor contains several assumptions that are often not applicable to specific ground conditions. There is also no standard procedure for safety factor determination, resulting in detrimental impacts on drilling operations. This paper provides an analysis of the standard methods and proposes two alternative analytical models to more accurately determine the hydraulic fracture point and acceptable drilling pressure. These alternative methods provide greater understanding of the interaction between the drilling pressures and the surrounding ground strength properties. This allows for more accurate determination of horizontal directional drilling limitations. A comparison is presented to determine the differences in characteristics and assumptions for each model. The impact of specific soil properties and factors is investigated by means of a sensitivity analysis to determine the most critical soil information for each model.

scholarly journals From the Vector to Scalar Perturbations Addition in the Stark Broadening Theory of Spectral Lines

Universe ◽  
2021 ◽  
Vol 7 (6) ◽  
pp. 176
Author(s):  
Valery Astapenko ◽  
Andrei Letunov ◽  
Valery Lisitsa
Keyword(s):  
Spectral Line ◽  
Stark Effect ◽  
Coulomb Field ◽  
Spectral Lines ◽  
Alternative Methods ◽  
Scalar Perturbation ◽  
Numerical Comparison ◽  
Line Shapes ◽  
Stark Effects ◽  
The Impact

The effect of plasma Coulomb microfied dynamics on spectral line shapes is under consideration. The analytical solution of the problem is unachievable with famous Chandrasekhar–Von-Neumann results up to the present time. The alternative methods are connected with modeling of a real ion Coulomb field dynamics by approximate models. One of the most accurate theories of ions dynamics effect on line shapes in plasmas is the Frequency Fluctuation Model (FFM) tested by the comparison with plasma microfield numerical simulations. The goal of the present paper is to make a detailed comparison of the FFM results with analytical ones for the linear and quadratic Stark effects in different limiting cases. The main problem is connected with perturbation additions laws known to be vector for small particle velocities (static line shapes) and scalar for large velocities (the impact limit). The general solutions for line shapes known in the frame of scalar perturbation additions are used to test the FFM procedure. The difference between “scalar” and “vector” models is demonstrated both for linear and quadratic Stark effects. It is shown that correct transition from static to impact limits for linear Stark-effect needs in account of the dependence of electric field jumping frequency in FFM on the field strengths. However, the constant jumping frequency is quite satisfactory for description of the quadratic Stark-effect. The detailed numerical comparison for spectral line shapes in the frame of both scalar and vector perturbation additions with and without jumping frequency field dependence for the linear and quadratic Stark effects is presented.

A Study on UV Filter Chemicals from Annex VII of European Union Directive 76/768/EEC, in the In Vitro 3T3 NRU Phototoxicity Test

1998 ◽  
Vol 26 (5) ◽  
pp. 679-708 ◽  
Author(s):  
Horst Spielmann ◽  
Michael Balls ◽  
Jack Dupuis ◽  
Wolfgang J. W. Pape ◽  
Odile de Silva ◽  
...  
Keyword(s):  
Neutral Red ◽  
Optimum Concentration ◽  
Alternative Methods ◽  
Uv Filter ◽  
Eu Directive ◽  
Optimum Concentration Range ◽  
The Impact ◽  
Positive Results

In 1996, the Scientific Committee on Cosmetology of DGXXIV of the European Commission asked the European Centre for the Validation of Alternative Methods to test eight UV filter chemicals from the 1995 edition of Annex VII of Directive 76/768/EEC in a blind trial in the in vitro 3T3 cell neutral red uptake phototoxicity (3T3 NRU PT) test, which had been scientifically validated between 1992 and 1996. Since all the UV filter chemicals on the positive list of EU Directive 76/768/EEC have been shown not to be phototoxic in vivo in humans under use conditions, only negative effects would be expected in the 3T3 NRU PT test. To balance the number of positive and negative chemicals, ten phototoxic and ten non-phototoxic chemicals were tested under blind conditions in four laboratories. Moreover, to assess the optimum concentration range for testing, information was provided on appropriate solvents and on the solubility of the coded chemicals. In this study, the phototoxic potential of test chemicals was evaluated in a prediction model in which either the Photoirritation Factor (PIF) or the Mean Photo Effect (MPE) were determined. The results obtained with both PIF and MPE were highly reproducible in the four laboratories, and the correlation between in vitro and in vivo data was almost perfect. All the phototoxic test chemicals provided a positive result at concentrations of 1μg/ml, while nine of the ten non-phototoxic chemicals gave clear negative results, even at the highest test concentrations. One of the UV filter chemicals gave positive results in three of the four laboratories only at concentrations greater than 100μg/ml; the other laboratory correctly identified all 20 of the test chemicals. An analysis of the impact that exposure concentrations had on the performance of the test revealed that the optimum concentration range in the 3T3 NRU PT test for determining the phototoxic potential of chemicals is between 0.1μg/ml and 10μg/ml, and that false positive results can be obtained at concentrations greater than 100μg/ml. Therefore, the positive results obtained with some of the UV filter chemicals only at concentrations greater than 100μg/ml do not indicate a phototoxic potential in vivo. When this information was taken into account during calculation of the overall predictivity of the 3T3 NRU PT test in the present study, an almost perfect correlation of in vitro versus in vivo results was obtained (between 95% and 100%), when either PIF or MPE were used to predict the phototoxic potential. The management team and participants therefore conclude that the 3T3 NRU PT test is a valid test for correctly assessing the phototoxic potential of UV filter chemicals, if the defined concentration limits are taken into account.

scholarly journals Conducting Population Health Research during the COVID-19 Pandemic: Impacts and Recommendations

2021 ◽  
Vol 13 (6) ◽  
pp. 3320
Author(s):  
Amy R. Villarosa ◽  
Lucie M. Ramjan ◽  
Della Maneze ◽  
Ajesh George
Keyword(s):  
Data Collection ◽  
Health Services ◽  
Data Quality ◽  
Population Health ◽  
Health Research ◽  
Alternative Methods ◽  
Residential Aged Care ◽  
Recruitment Methods ◽  
Face To Face ◽  
The Impact

The COVID-19 pandemic has resulted in many changes, including restrictions on indoor gatherings and visitation to residential aged care facilities, hospitals and certain communities. Coupled with potential restrictions imposed by health services and academic institutions, these changes may significantly impact the conduct of population health research. However, the continuance of population health research is beneficial for the provision of health services and sometimes imperative. This paper discusses the impact of COVID-19 restrictions on the conduct of population health research. This discussion unveils important ethical considerations, as well as potential impacts on recruitment methods, face-to-face data collection, data quality and validity. In addition, this paper explores potential recruitment and data collection methods that could replace face-to-face methods. The discussion is accompanied by reflections on the challenges experienced by the authors in their own research at an oral health service during the COVID-19 pandemic and alternative methods that were utilised in place of face-to-face methods. This paper concludes that, although COVID-19 presents challenges to the conduct of population health research, there is a range of alternative methods to face-to-face recruitment and data collection. These alternative methods should be considered in light of project aims to ensure data quality is not compromised.

scholarly journals Exploring diversification drivers in golden orbweavers

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Eva Turk ◽  
Simona Kralj-Fišer ◽  
Matjaž Kuntner
Keyword(s):  
Environmental Factors ◽  
Sexual Size Dimorphism ◽  
Male Body ◽  
Diversification Rates ◽  
Size Dimorphism ◽  
Extinction Rates ◽  
Intermediate Phenotypes ◽  
Dispersal Propensity ◽  
The Tropics ◽  
Class Models

AbstractHeterogeneity in species diversity is driven by the dynamics of speciation and extinction, potentially influenced by organismal and environmental factors. Here, we explore macroevolutionary trends on a phylogeny of golden orbweavers (spider family Nephilidae). Our initial inference detects heterogeneity in speciation and extinction, with accelerated extinction rates in the extremely sexually size dimorphic Nephila and accelerated speciation in Herennia, a lineage defined by highly derived, arboricolous webs, and pronounced island endemism. We evaluate potential drivers of this heterogeneity that relate to organisms and their environment. Primarily, we test two continuous organismal factors for correlation with diversification in nephilids: phenotypic extremeness (female and male body length, and sexual size dimorphism as their ratio) and dispersal propensity (through range sizes as a proxy). We predict a bell-shaped relationship between factor values and speciation, with intermediate phenotypes exhibiting highest diversification rates. Analyses using SSE-class models fail to support our two predictions, suggesting that phenotypic extremeness and dispersal propensity cannot explain patterns of nephilid diversification. Furthermore, two environmental factors (tropical versus subtropical and island versus continental species distribution) indicate only marginal support for higher speciation in the tropics. Although our results may be affected by methodological limitations imposed by a relatively small phylogeny, it seems that the tested organismal and environmental factors play little to no role in nephilid diversification. In the phylogeny of golden orbweavers, the recent hypothesis of universal diversification dynamics may be the simplest explanation of macroevolutionary patterns.

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