scholarly journals Macroevolutionary diversification rates show time dependency

2019 ◽  
Vol 116 (15) ◽  
pp. 7403-7408 ◽  
Author(s):  
L. Francisco Henao Diaz ◽  
Luke J. Harmon ◽  
Mauro T. C. Sugawara ◽  
Eliot T. Miller ◽  
Matthew W. Pennell
Keyword(s):  
Time Series ◽  
Phylogenetic Trees ◽  
Scaling Law ◽  
Sensitivity Analyses ◽  
Time Dependency ◽  
Large Collection ◽  
Deep Time ◽  
Diversification Rates ◽  
Extinction Rates ◽  
Time Scaling

For centuries, biologists have been captivated by the vast disparity in species richness between different groups of organisms. Variation in diversity is widely attributed to differences between groups in how fast they speciate or go extinct. Such macroevolutionary rates have been estimated for thousands of groups and have been correlated with an incredible variety of organismal traits. Here we analyze a large collection of phylogenetic trees and fossil time series and describe a hidden generality among these seemingly idiosyncratic results: speciation and extinction rates follow a scaling law in which both depend on the age of the group in which they are measured, with the fastest rates in the youngest clades. Using a series of simulations and sensitivity analyses, we demonstrate that the time dependency is unlikely to be a result of simple statistical artifacts. As such, this time scaling is likely a genuine feature of the tree of life, hinting that the dynamics of biodiversity over deep time may be driven in part by surprisingly simple and general principles.

scholarly journals Macroevolutionary diversification rates show time-dependency

2018 ◽  
Author(s):  
Luis Francisco Henao Diaz ◽  
Luke J. Harmon ◽  
Mauro T.C. Sugawara ◽  
Eliot I Miller ◽  
Matthew W. Pennell
Keyword(s):  
Time Series ◽  
Phylogenetic Trees ◽  
Scaling Law ◽  
Sensitivity Analyses ◽  
Time Dependency ◽  
Large Collection ◽  
Deep Time ◽  
Diversification Rates ◽  
Extinction Rates ◽  
Time Scaling

For centuries, biologists have been captivated by the vast disparity in species richness between different groups of organisms. Variation in diversity is widely attributed to differences between groups in how fast they speciate or go extinct. Such macroevolutionary rates have been estimated for thousands of groups and have been correlated with an incredible variety of organismal traits. Here we analyze a large collection of phylogenetic trees and fossil time series and describe a hidden generality amongst these seemingly idiosyncratic results: speciation and extinction rates follow a scaling law where both depend on the age of the group in which they are measured, with the fastest rates in the youngest clades. Using a series of simulations and sensitivity analyses, we demonstrate that the time-dependency is unlikely to be a result of simple statistical artifacts. As such, this time-scaling is likely a genuine feature of the Tree of Life -- hinting that the dynamics of biodiversity over deep time may be driven, in part, by surprisingly simple and general principles.

scholarly journals Pulled Diversification Rates, Lineage-Through-Time Plots and Modern Macroevolutionary Modelling

2021 ◽  
Author(s):  
Andrew J. Helmstetter ◽  
Sylvain Glemin ◽  
Jos Käfer ◽  
Rosana Zenil-Ferguson ◽  
Hervé Sauquet ◽  
...  
Keyword(s):  
Infinite Number ◽  
Scientific Community ◽  
Phylogenetic Trees ◽  
Data Availability ◽  
Time Dependent ◽  
Evolutionary Processes ◽  
Diversification Rates ◽  
Extinction Rates ◽  
Extant Species ◽  
Technical Considerations

AbstractEstimating time-dependent rates of speciation and extinction from dated phylogenetic trees of extant species (timetrees), and determining how and why they vary is key to understanding how ecological and evolutionary processes shape biodiversity. Due to an increasing availability of phylogenies, a growing number of process-based methods relying on the birth-death model have been developed in the last decade to address a variety of questions in macroevolution. However, this methodological progress has regularly been criticised such that one may wonder how reliable the estimations of speciation and extinction rates are. In particular, using lineage-through-time (LTT) plots, a recent study (Louca and Pennell, 2020) has shown that there are an infinite number of equally likely diversification scenarios that can generate any timetree. This has led to questioning whether or not diversification rates should be estimated at all. Here we summarize, clarify, and highlight technical considerations on recent findings regarding the capacity of models and inferences to disentangle diversification histories. Using simulations we demonstrate the characteristics of pulled diversification rates and their utility. We recognize the recent findings are a step forward in understanding the behavior of macroevolutionary modelling, but they in no way suggest we should abandon diversification modelling altogether. On the contrary, the study of macroevolution using phylogenies has never been more exciting and promising than today. We still face important limitations in regard to data availability and methodological shortcomings, but by acknowledging them we can better target our joint efforts as a scientific community.

scholarly journals Diversification rates and the latitudinal gradient of diversity in mammals

2012 ◽  
Vol 279 (1745) ◽  
pp. 4148-4155 ◽  
Author(s):  
Víctor Soria-Carrasco ◽  
Jose Castresana
Keyword(s):  
Species Richness ◽  
Species Distribution ◽  
Phylogenetic Trees ◽  
Latitudinal Gradient ◽  
Diversification Rate ◽  
Independent Contrasts ◽  
Diversification Rates ◽  
Extinction Rates ◽  
Phylogenetically Independent Contrasts ◽  
Distribution Ranges

The latitudinal gradient of species richness has frequently been attributed to higher diversification rates of tropical groups. In order to test this hypothesis for mammals, we used a set of 232 genera taken from a mammalian supertree and, additionally, we reconstructed dated Bayesian phylogenetic trees of 100 genera. For each genus, diversification rate was estimated taking incomplete species sampling into account and latitude was assigned considering the heterogeneity in species distribution ranges. For both datasets, we found that the average diversification rate was similar among all latitudinal bands. Furthermore, when we used phylogenetically independent contrasts, we did not find any significant correlation between latitude and diversification parameters, including different estimates of speciation and extinction rates. Thus, other factors, such as the dynamics of dispersal through time, may be required to explain the latitudinal gradient of diversity in mammals.

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 Pulled Diversification Rates, Lineages-Through-Time Plots and Modern Macroevolutionary Modelling

2021 ◽  
Author(s):  
Andrew J Helmstetter ◽  
Sylvain Glemin ◽  
Jos Käfer ◽  
Rosana Zenil-Ferguson ◽  
Herv Sauquet ◽  
...  
Keyword(s):  
Infinite Number ◽  
Scientific Community ◽  
Phylogenetic Trees ◽  
Data Availability ◽  
Time Dependent ◽  
Evolutionary Processes ◽  
Diversification Rates ◽  
Extinction Rates ◽  
Extant Species ◽  
Technical Considerations

Abstract Estimating time-dependent rates of speciation and extinction from dated phylogenetic trees of extant species (timetrees), and determining how and why they vary, is key to understanding how ecological and evolutionary processes shape biodiversity. Due to an increasing availability of phylogenetic trees, a growing number of process-based methods relying on the birth-death model have been developed in the last decade to address a variety of questions in macroevolution. However, this methodological progress has regularly been criticised such that one may wonder how reliable the estimations of speciation and extinction rates are. In particular, using lineages-through-time (LTT) plots, a recent study (Louca and Pennell, 2020) has shown that there are an infinite number of equally likely diversification scenarios that can generate any timetree. This has led to questioning whether or not diversification rates should be estimated at all. Here we summarize, clarify, and highlight technical considerations on recent findings regarding the capacity of models to disentangle diversification histories. Using simulations we illustrate the characteristics of newly-proposed “pulled rates” and their utility. We recognize that the recent findings are a step forward in understanding the behavior of macroevolutionary modelling, but they in no way suggest we should abandon diversification modelling altogether. On the contrary, the study of macroevolution using phylogenetic trees has never been more exciting and promising than today. We still face important limitations in regard to data availability and methods, but by acknowledging them we can better target our joint efforts as a scientific community.

scholarly journals Deep time series models for scarce data

2021 ◽  
Author(s):  
Qiyao Wang ◽  
Ahmed Farahat ◽  
Chetan Gupta ◽  
Shuai Zheng
Keyword(s):  
Time Series ◽  
Time Series Models ◽  
Deep Time ◽  
Scarce Data

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.

scholarly journals Association Between PM2.5 and Daily Hospital Admissions for Heart Failure: A Time-Series Analysis in Beijing

2018 ◽  
Vol 15 (10) ◽  
pp. 2217 ◽  
Author(s):  
Man Li ◽  
Yao Wu ◽  
Yao-Hua Tian ◽  
Ya-Ying Cao ◽  
Jing Song ◽  
...  
Keyword(s):  
Heart Failure ◽  
Time Series ◽  
Degrees Of Freedom ◽  
Hospital Admissions ◽  
Scientific Evidence ◽  
Poisson Model ◽  
Sensitivity Analyses ◽  
Calendar Time ◽  
Medical Claim ◽  
Increased Risk

There is little evidence that acute exposure to fine particulate matter (PM2.5) impacts the rate of hospitalization for congestive heart failure (CHF) in developing countries. The primary purpose of the present retrospective study was to evaluate the short-term association between ambient PM2.5 and hospitalization for CHF in Beijing, China. A total of 15,256 hospital admissions for CHF from January 2010 to June 2012 were identified from Beijing Medical Claim Data for Employees and a time-series design with generalized additive Poisson model was used to assess the obtained data. We found a clear significant exposure response association between PM2.5 and the number of hospitalizations for CHF. Increasing PM2.5 daily concentrations by 10 μg/m3 caused a 0.35% (95% CI, 0.06–0.64%) increase in the number of CHF admissions on the same day. We also found that female and older patients were more susceptible to PM2.5. These associations remained significant in sensitivity analyses involving changing the degrees of freedom of calendar time, temperature, and relative humidity. PM2.5 was associated with significantly increased risk of hospitalization for CHF in this citywide study. These findings may contribute to the limited scientific evidence about the acute impacts of PM2.5 on CHF in China.

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.

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