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 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 The choice of tree prior and molecular clock does not substantially affect phylogenetic inferences of diversification rates

2018 ◽  
Author(s):  
Brice A. J. Sarver ◽  
Matthew W. Pennell ◽  
Joseph W. Brown ◽  
Sara Keeble ◽  
Kayla M. Hardwick ◽  
...  
Keyword(s):  
Molecular Clock ◽  
Substitution Rate ◽  
Phylogenetic Trees ◽  
Sequence Data ◽  
Parameter Estimates ◽  
Molecular Clocks ◽  
Estimation Of Parameters ◽  
Rate Heterogeneity ◽  
Diversification Rates ◽  
The Impact

AbstractComparative methods allow researchers to make inferences about evolutionary processes and patterns from phylogenetic trees. In Bayesian phylogenetics, estimating a phylogeny requires specifying priors on parameters characterizing the branching process and rates of substitution among lineages, in addition to others. However, the effect that the selection of these priors has on the inference of comparative parameters has not been thoroughly investigated. Such uncertainty may systematically bias phylogenetic reconstruction and, subsequently, parameter estimation. Here, we focus on the impact of priors in Bayesian phylogenetic inference and evaluate how they affect the estimation of parameters in macroevolutionary models of lineage diversification. Specifically, we use BEAST to simulate trees under combinations of tree priors and molecular clocks, simulate sequence data, estimate trees, and estimate diversification parameters (e.g., speciation rates and extinction rates) from these trees. When substitution rate heterogeneity is large, parameter estimates deviate substantially from those estimated under the simulation conditions when not captured by an appropriate choice of relaxed molecular clock. However, in general, we find that the choice of tree prior and molecular clock has relatively little impact on the estimation of diversification rates insofar as the sequence data are sufficiently informative and substitution rate heterogeneity among lineages is low-to-moderate.

scholarly journals A Bayesian Approach for Estimating Branch-Specific Speciation and Extinction Rates

2019 ◽  
Author(s):  
Sebastian Höhna ◽  
William A. Freyman ◽  
Zachary Nolen ◽  
John P. Huelsenbeck ◽  
Michael R. May ◽  
...  
Keyword(s):  
Prior Distribution ◽  
Phylogenetic Trees ◽  
Data Augmentation ◽  
Simulated Data ◽  
Monte Carlo Sampling ◽  
Fixed Number ◽  
Diversification Rate ◽  
Diversification Rates ◽  
Extinction Rates ◽  
Birth Death

AbstractSpecies richness varies considerably among the tree of life which can only be explained by heterogeneous rates of diversification (speciation and extinction). Previous approaches use phylogenetic trees to estimate branch-specific diversification rates. However, all previous approaches disregard diversification-rate shifts on extinct lineages although 99% of species that ever existed are now extinct. Here we describe a lineage-specific birth-death-shift process where lineages, both extant and extinct, may have heterogeneous rates of diversification. To facilitate probability computation we discretize the base distribution on speciation and extinction rates into k rate categories. The fixed number of rate categories allows us to extend the theory of state-dependent speciation and extinction models (e.g., BiSSE and MuSSE) to compute the probability of an observed phylogeny given the set of speciation and extinction rates. To estimate branch-specific diversification rates, we develop two independent and theoretically equivalent approaches: numerical integration with stochastic character mapping and data-augmentation with reversible-jump Markov chain Monte Carlo sampling. We validate the implementation of the two approaches in RevBayes using simulated data and an empirical example study of primates. In the empirical example, we show that estimates of the number of diversification-rate shifts are, unsurprisingly, very sensitive to the choice of prior distribution. Instead, branch-specific diversification rate estimates are less sensitive to the assumed prior distribution on the number of diversification-rate shifts and consistently infer an increased rate of diversification for Old World Monkeys. Additionally, we observe that as few as 10 diversification-rate categories are sufficient to approximate a continuous base distribution on diversification rates. In conclusion, our implementation of the lineage-specific birth-death-shift model in RevBayes provides biologists with a method to estimate branch-specific diversification rates under a mathematically consistent model.

scholarly journals The choice of tree prior and molecular clock does not substantially affect phylogenetic inferences of diversification rates

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6334 ◽  
Author(s):  
Brice A.J. Sarver ◽  
Matthew W. Pennell ◽  
Joseph W. Brown ◽  
Sara Keeble ◽  
Kayla M. Hardwick ◽  
...  
Keyword(s):  
Molecular Clock ◽  
Substitution Rate ◽  
Phylogenetic Trees ◽  
Sequence Data ◽  
Phylogenetic Reconstruction ◽  
Molecular Clocks ◽  
Estimation Of Parameters ◽  
Rate Heterogeneity ◽  
Diversification Rates ◽  
The Impact

Comparative methods allow researchers to make inferences about evolutionary processes and patterns from phylogenetic trees. In Bayesian phylogenetics, estimating a phylogeny requires specifying priors on parameters characterizing the branching process and rates of substitution among lineages, in addition to others. Accordingly, characterizing the effect of prior selection on phylogenies is an active area of research. The choice of priors may systematically bias phylogenetic reconstruction and, subsequently, affect conclusions drawn from the resulting phylogeny. Here, we focus on the impact of priors in Bayesian phylogenetic inference and evaluate how they affect the estimation of parameters in macroevolutionary models of lineage diversification. Specifically, we simulate trees under combinations of tree priors and molecular clocks, simulate sequence data, estimate trees, and estimate diversification parameters (e.g., speciation and extinction rates) from these trees. When substitution rate heterogeneity is large, diversification rate estimates deviate substantially from those estimated under the simulation conditions when not captured by an appropriate choice of relaxed molecular clock. However, in general, we find that the choice of tree prior and molecular clock has relatively little impact on the estimation of diversification rates insofar as the sequence data are sufficiently informative and substitution rate heterogeneity among lineages is low-to-moderate.

scholarly journals A Threat of Customer Incivility and Job Stress to Hotel Employee Retention: Do Supervisor and Co-Worker Supports Reduce Turnover Rates?

2021 ◽  
Vol 18 (12) ◽  
pp. 6616
Author(s):  
Hyunah Chung ◽  
Wei Quan ◽  
Bonhak Koo ◽  
Antonio Ariza-Montes ◽  
Alejandro Vega-Muñoz ◽  
...  
Keyword(s):  
Job Stress ◽  
Turnover Intention ◽  
Supervisor Support ◽  
Demographic Variables ◽  
Point Of View ◽  
Frontline Employees ◽  
Turnover Rates ◽  
Negative Behaviors ◽  
Perceived Supervisor Support ◽  
The Impact

The study investigates the impact of customer incivility, job stress, perceived supervisor support, and perceived co-worker support on the turnover intention of frontline employees. A survey-questionnaire approach was used to collect the point of view of frontline employees that work in five-star hotels in a metropolitan city of Korea. Four independent variables that were extracted from valid theoretical backgrounds along with four demographic variables were used in the study. The regression analysis was conducted to test the hypotheses, which revealed that job stress directly affected the employees’ desires to leave their organization. It also showed that perceived supervisor support mitigates employee turnover, and there were significant correlations between turnover intention with the employees’ marital status and job position. Gender and years of service did not affect the employees’ thinking of quitting their job. Our findings help hotel entrepreneurs better understand how to deal with customer incivility and employee job stress, and better comprehend the factors that minimize employees’ negative behaviors for the organization.

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 ACDC: Analysis of Congruent Diversification Classes

2022 ◽  
Author(s):  
Sebastian Hoehna ◽  
Bjoern Tore Kopperud ◽  
Andrew F Magee
Keyword(s):  
Congruence Class ◽  
R Package ◽  
Rate Function ◽  
Diversification Rate ◽  
Extinction Rate ◽  
Diversification Rates ◽  
Common Features ◽  
Alternative Hypotheses ◽  
Rate Functions ◽  
Congruence Classes

Diversification rates inferred from phylogenies are not identifiable. There are infinitely many combinations of speciation and extinction rate functions that have the exact same likelihood score for a given phylogeny, building a congruence class. The specific shape and characteristics of such congruence classes have not yet been studied. Whether speciation and extinction rate functions within a congruence class share common features is also not known. Instead of striving to make the diversification rates identifiable, we can embrace their inherent non-identifiable nature. We use two different approaches to explore a congruence class: (i) testing of specific alternative hypotheses, and (ii) randomly sampling alternative rate function within the congruence class. Our methods are implemented in the open-source R package ACDC (https://github.com/afmagee/ACDC). ACDC provides a flexible approach to explore the congruence class and provides summaries of rate functions within a congruence class. The summaries can highlight common trends, i.e. increasing, flat or decreasing rates. Although there are infinitely many equally likely diversification rate functions, these can share common features. ACDC can be used to assess if diversification rate patterns are robust despite non-identifiability. In our example, we clearly identify three phases of diversification rate changes that are common among all models in the congruence class. Thus, congruence classes are not necessarily a problem for studying historical patterns of biodiversity from phylogenies.

Estimating Diversification Rates on Incompletely Sampled Phylogenies: Theoretical Concerns and Practical Solutions

2019 ◽  
Vol 69 (3) ◽  
pp. 602-611 ◽  
Author(s):  
Jonathan Chang ◽  
Daniel L Rabosky ◽  
Michael E Alfaro
Keyword(s):  
Statistical Power ◽  
Likelihood Function ◽  
Point Of View ◽  
Death Process ◽  
Rate Variation ◽  
Sampled Data ◽  
Diversification Rates ◽  
Sampling Fraction ◽  
Incomplete Sampling ◽  
Birth Death

Abstract Molecular phylogenies are a key source of information about the tempo and mode of species diversification. However, most empirical phylogenies do not contain representatives of all species, such that diversification rates are typically estimated from incompletely sampled data. Most researchers recognize that incomplete sampling can lead to biased rate estimates, but the statistical properties of methods for accommodating incomplete sampling remain poorly known. In this point of view, we demonstrate theoretical concerns with the widespread use of analytical sampling corrections for sparsely sampled phylogenies of higher taxonomic groups. In particular, corrections based on “sampling fractions” can lead to low statistical power to infer rate variation when it is present, depending on the likelihood function used for inference. In the extreme, the sampling fraction correction can lead to spurious patterns of diversification that are driven solely by unbalanced sampling across the tree in concert with low overall power to infer shifts. Stochastic polytomy resolution provides an alternative to sampling fraction approaches that avoids some of these biases. We show that stochastic polytomy resolvers can greatly improve the power of common analyses to estimate shifts in diversification rates. We introduce a new stochastic polytomy resolution method (Taxonomic Addition for Complete Trees [TACT]) that uses birth–death-sampling estimators across an ultrametric phylogeny to estimate branching times for unsampled taxa, with taxonomic information to compatibly place new taxa onto a backbone phylogeny. We close with practical recommendations for diversification inference under several common scenarios of incomplete sampling. [Birth–death process; diversification; incomplete sampling; phylogenetic uncertainty; rate heterogeneity; rate shifts; stochastic polytomy resolution.]

scholarly journals Age and rate of diversification of the Hawaiian silversword alliance (Compositae)

1998 ◽  
Vol 95 (16) ◽  
pp. 9402-9406 ◽  
Author(s):  
Bruce G. Baldwin ◽  
Michael J. Sanderson
Keyword(s):  
Common Ancestor ◽  
Error Variance ◽  
Diversification Rate ◽  
Recent Common Ancestor ◽  
Divergence Times ◽  
Sequence Evolution ◽  
Most Recent Common Ancestor ◽  
History Of ◽  
Fossil Records ◽  
Fossil Data

Comparisons between insular and continental radiations have been hindered by a lack of reliable estimates of absolute diversification rates in island lineages. We took advantage of rate-constant rDNA sequence evolution and an “external” calibration using paleoclimatic and fossil data to determine the maximum age and minimum diversification rate of the Hawaiian silversword alliance (Compositae), a textbook example of insular adaptive radiation in plants. Our maximum-age estimate of 5.2 ± 0.8 million years ago for the most recent common ancestor of the silversword alliance is much younger than ages calculated by other means for the Hawaiian drosophilids, lobelioids, and honeycreepers and falls approximately within the history of the modern high islands (≤5.1 ± 0.2 million years ago). By using a statistically efficient estimator that reduces error variance by incorporating clock-based estimates of divergence times, a minimum diversification rate for the silversword alliance was estimated to be 0.56 ± 0.17 species per million years. This exceeds average rates of more ancient continental radiations and is comparable to peak rates in taxa with sufficiently rich fossil records that changes in diversification rate can be reconstructed.

Critical Factors for Field Staff: The Relationship Between Burnout, Coping, and Vocational Purpose

2019 ◽  
Vol 42 (4) ◽  
pp. 398-416
Author(s):  
Alexandra Z. Kolaski ◽  
Jennifer M. Taylor
Keyword(s):  
Behavioral Health Care ◽  
Security Assessment ◽  
Turnover Rates ◽  
Field Staff ◽  
Workplace Satisfaction ◽  
Key Characteristics ◽  
Outdoor Behavioral Health Care ◽  
Confirmatory Factor ◽  
The Impact ◽  
The Relationship

Background: Outdoor Behavioral Health Care (OBH) programs rely on field staff (FS) for the daily management of program activities, client safety and security, assessment information, and therapeutic intervention. Purpose: Given research that indicates turnover rates among FS are high, the present study was designed to evaluate components of resilience and burnout among FS that may help OBH programs retain FS. Methodology/Approach: Confirmatory factor analysis was used to empirically examine the impact of McEwan’s Workplace Resilience Model factors on FS resilience. Findings/Conclusions: A well-fitting model was developed to explain relationships between burnout, coping skills, and purpose among FS. Important links between vocational purpose, coping, and burnout were found. Implications: This article concludes by discussing implications and recommendations for OBH programs, in support of FS retention and workplace satisfaction, including the importance of creating workplace social and physical health support systems and key characteristics of resilient FS.

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