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 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 Prior hypotheses or regularization allow inference of diversification histories from extant timetrees

2020 ◽  
Author(s):  
Hélène Morlon ◽  
Florian Hartig ◽  
Stéphane Robin
Keyword(s):  
Model Selection ◽  
Infinite Number ◽  
Selection Procedure ◽  
Data Driven ◽  
Model Selection Procedure ◽  
Extinction Rates ◽  
Extant Species ◽  
Over Time

AbstractPhylogenies of extant species are widely used to study past diversification dynamics1. The most common approach is to formulate a set of candidate models representing evolutionary hypotheses for how and why speciation and extinction rates in a clade changed over time, and compare those models through their probability to have generated the corresponding empirical tree. Recently, Louca & Pennell2 reported the existence of an infinite number of ‘congruent’ models with potentially markedly different diversification dynamics, but equal likelihood, for any empirical tree (see also Lambert & Stadler3). Here we explore the implications of these results, and conclude that they neither undermine the hypothesis-driven model selection procedure widely used in the field nor show that speciation and extinction dynamics cannot be investigated from extant timetrees using a data-driven procedure.

scholarly journals The probability distribution of the reconstructed phylogenetic tree with occurrence data

2019 ◽  
Author(s):  
Ankit Gupta ◽  
Marc Manceau ◽  
Timothy Vaughan ◽  
Mustafa Khammash ◽  
Tanja Stadler
Keyword(s):  
Probability Density ◽  
Phylogenetic Trees ◽  
Joint Probability ◽  
Death Process ◽  
Joint Analysis ◽  
Successive Sampling ◽  
Sampling Schemes ◽  
Extinction Rates ◽  
Case Count ◽  
Extant Species

AbstractWe consider a homogeneous birth-death process with incomplete sampling. Three successive sampling schemes are considered. First, individuals can be sampled through time and included in the tree. Second, they can be occurrences which are sampled through time and not included in the tree. Third, individuals reaching present day can be sampled and included in the tree. Upon sampling, individuals are removed (i.e. die).The outcome of the process is thus composed of the reconstructed evolutionary tree spanning all individuals sampled and included in the tree, and a timeline of occurrence events which are not placed along the tree. We derive a formula allowing one to compute the joint probability density of these, which can readily be used to perform maximum likelihood or Bayesian estimation of the parameters of the model.In the context of epidemiology, our probability density allows us to estimate transmission rates through a joint analysis of epidemiological case count data and phylogenetic trees reconstructed from pathogen sequences. Within macroevolution, our equations are the basis for taking into account fossil occurrences from paleontological databases together with extant species phylogenies for estimating speciation and extinction rates. Thus, we provide the theoretical framework for bridging not only the gap between phylogenetics and epidemiology, but also the gap between phylogenetics and paleontology.

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 The definition and macroevolutionary study of planktic foraminiferal higher taxa

1992 ◽  
Vol 6 ◽  
pp. 133-133
Author(s):  
Steven D'Hondt
Keyword(s):  
Phylogenetic Trees ◽  
Planktic Foraminifera ◽  
Fossil Species ◽  
Extinction Rates ◽  
Higher Taxa ◽  
Late Paleocene ◽  
Extant Species ◽  
Stable Isotopic ◽  
Early Paleocene ◽  
Surface Dwelling

Planktic foraminiferal species are generally assigned to higher taxa on the basis of shared morphologic characters and stratigraphic age. These assignments are usually justified on the basis of apparent phyletic relationships. Extant species assigned to the same genera usually exhibit similar trophic and reproductive behavior and are associated with similar watermasses. Paleogeographic and stable isotopic data suggest that coeval fossil species also generally exhibit similar paleoecologic and paleoceanographic associations within well-constrained genera.Despite shared morphologic characters and stratigraphic and paleoenvironmental associations, many higher taxa of planktic foraminifera are not believed to be monophyletic. Many superspecific taxa are widely accepted as paraphyletic (i.e. Guembelitria, Heterohelix). Such paraphyly has commonly resulted from maintaining a different generic or familial name for descendant species that diverge strongly from their ancestral bauplan. Additionally, some higher taxa appear to be polyphyletic (i.e. Eoglobigerinidae, Globorotalia).As presently defined, superspecific taxa–commonly paraphyletic–can generally be used to examine relative radiation and extinction rates within and between different planktic foraminiferal adaptive zones. For example, analysis of Paleocene genera demonstrates rapid earliest Paleocene origination and radiation of sea-surface-dwelling and deeper-dwelling biserial and trochospiral genera. This earliest Paleocene radiation is quickly followed by disappearance of these surface-dwelling genera and some deeper-dwelling genera, in turn followed by major radiation within new surface-dwelling trochospiral genera in the mid and Late Paleocene. Such analysis documents the relative diversity and succession of major adaptive groups, regardless of their phylogenetic relationships.The phyletic status of existing superspecific taxa does not preclude macroevolutionary study of monophyletic groups—or require that presently paraphyletic taxa be subsumed into larger monophyletic taxa. It simply requires that study of monophyletic groups be explicitly based on cladograms or phylogenetic trees. Such studies can address topics of clear macroevolutionary interest, including (i) the relative diversity and longevity of different monophyletic groups and (ii) general patterns of origination and extinction within clades. Additionally, while phylogenetic analysis is not necessary to determine patterns of succession and diversity of within and between adaptive groups, it can amplify our understanding of such patterns. For example, the earliest Paleocene appears to be marked by extremely rapid radiation within two monophyletic groups. The first reaches peak diversity within the earliest Paleocene and dominates earliest Paleocene planktic foraminiferal assemblages, but decreases radically in diversity and abundance within the Early Paleocene. The second continues to diversify throughout the Paleocene and dominates mid and Late Paleocene faunas. Consideration of phylogenetic and paleoecologic relationships within and between both monophyletic groups clearly reveals convergent evolution of deep and surface-dwelling morphotypes, and of biserial and trochospiral forms.

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 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 LINEAR TIME-DEPENDENT INVARIANTS FOR SCALAR FIELDS AND NOETHER’S THEOREM

1994 ◽  
Vol 09 (19) ◽  
pp. 1785-1790 ◽  
Author(s):  
O. CASTAÑOS ◽  
R. LÓPEZ-PEÑA ◽  
V.I. MAN’KO
Keyword(s):  
Scalar Field ◽  
Infinite Number ◽  
Linear Time ◽  
Scalar Fields ◽  
Time Dependent ◽  
Noether’S Theorem ◽  
Noether's Theorem

The infinite number of time-dependent linear in field and conjugated momenta invariants is derived for the scalar field using the Noether’s theorem procedure.

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