Total-Evidence Dating and the Fossilized Birth–Death Model

2020 ◽  
pp. 175-193
Author(s):  
Alexandra Gavryushkina ◽  
Chi Zhang
Keyword(s):  
Total Evidence ◽  
Birth Death

scholarly journals Bayesian Node Dating based on Probabilities of Fossil Sampling Supports Trans-Atlantic Dispersal of Cichlid Fishes

2016 ◽  
Author(s):  
Michael Matschiner ◽  
Zuzana Musilová ◽  
Julia M I Barth ◽  
Zuzana Starostová ◽  
Walter Salzburger ◽  
...  
Keyword(s):  
Sequence Data ◽  
Sampling Rate ◽  
Divergence Time ◽  
Time Estimation ◽  
Total Evidence ◽  
Teleost Fishes ◽  
New Approach ◽  
Divergence Time Estimation ◽  
Age Estimates ◽  
Birth Death

Divergence-time estimation based on molecular phylogenies and the fossil record has provided insights into fundamental questions of evolutionary biology. In Bayesian node dating, phylogenies are commonly time calibrated through the specification of calibration densities on nodes representing clades with known fossil occurrences. Unfortunately, the optimal shape of these calibration densities is usually unknown and they are therefore often chosen arbitrarily, which directly impacts the reliability of the resulting age estimates. As possible solutions to this problem, two non-exclusive alternative approaches have recently been developed, the "fossilized birth-death" model and "total-evidence dating". While these approaches have been shown to perform well under certain conditions, they require including all (or a random subset) of the fossils of each clade in the analysis, rather than just relying on the oldest fossils of clades. In addition, both approaches assume that fossil records of different clades in the phylogeny are all the product of the same underlying fossil sampling rate, even though this rate has been shown to differ strongly between higher-level taxa. We here develop a flexible new approach to Bayesian node dating that combines advantages of traditional node dating and the fossilized birth-death model. In our new approach, calibration densities are defined on the basis of first fossil occurrences and sampling rate estimates that can be specified separately for all clades. We verify our approach with a large number of simulated datasets, and compare its performance to that of the fossilized birth death model. We find that our approach produces reliable age estimates that are robust to model violation, on par with the fossilized birth-death model. By applying our approach to a large dataset including sequence data from over 1000 species of teleost fishes as well as 147 carefully selected fossil constraints, we recover a timeline of teleost diversification that is incompatible with previously assumed vicariant divergences of freshwater fishes. Our results instead provide strong evidence for trans-oceanic dispersal of cichlids and other groups of teleost fishes.

scholarly journals A Simulation-Based Evaluation of Total-Evidence Dating Under the Fossilized Birth-Death Process

2018 ◽  
Author(s):  
Arong Luo ◽  
David A. Duchêne ◽  
Chi Zhang ◽  
Chao-Dong Zhu ◽  
Simon Y.W. Ho
Keyword(s):  
Morphological Characters ◽  
Nucleotide Sequences ◽  
Tree Topology ◽  
Molecular Dating ◽  
Total Evidence ◽  
Morphological Data ◽  
Death Process ◽  
Nucleotide Sequence Data ◽  
Wide Range ◽  
Birth Death

AbstractBayesian molecular dating is widely used to study evolutionary timescales. This procedure usually involves phylogenetic analysis of nucleotide sequence data, with fossil-based calibrations applied as age constraints on internal nodes of the tree. An alternative approach is Bayesian total-evidence dating, which involves the joint analysis of molecular data from present-day taxa and morphological data from both extant and fossil taxa. Part of its appeal stems from the fossilized birth-death process, which provides a model of lineage diversification for the prior on the tree topology and node times. However, total-evidence dating faces a number of considerable challenges, especially those associated with fossil sampling and evolutionary models for morphological characters. We conducted a simulation study to evaluate the performance of total-evidence dating with the fossilized birth-death model. We simulated fossil occurrences and the evolution of nucleotide sequences and morphological characters under a wide range of conditions. Our analyses show that fossil occurrences have a greater influence than the degree of among-lineage rate variation or the number of morphological characters on estimates of node times and the tree topology. Total-evidence dating generally performs well in recovering the relationships among extant taxa, but has difficulties in correctly placing fossil taxa in the tree and identifying the number of sampled ancestors. The method yields accurate estimates of the origin time of the fossilized birth-death process and the ages of the root and crown group, although the precision of these estimates varies with the probability of fossil occurrence. The exclusion of morphological characters results in a slight overestimation of node times, whereas the exclusion of nucleotide sequences has a negative impact on inference of the tree topology. Overall, our results provide a detailed view of the performance of total-evidence dating, which will inform further development of the method and its application to key questions in evolutionary biology.

scholarly journals A skyline birth-death process for inferring the population size from a reconstructed tree with occurrences

2020 ◽  
Author(s):  
Jérémy Andréoletti ◽  
Antoine Zwaans ◽  
Rachel C. M. Warnock ◽  
Gabriel Aguirre-Fernández ◽  
Joëlle Barido-Sottani ◽  
...  
Keyword(s):  
Population Size ◽  
Total Evidence ◽  
Morphological Data ◽  
Death Process ◽  
Model Parameters ◽  
Large Set ◽  
The Past ◽  
Population Sizes ◽  
Past Population ◽  
Birth Death

AbstractPhylodynamic models generally aim at jointly inferring phylogenetic relationships, model parameters, and more recently, population size through time for clades of interest, based on molecular sequence data. In the fields of epidemiology and macroevolution these models can be used to estimate, respectively, the past number of infected individuals (prevalence) or the past number of species (paleodiversity) through time. Recent years have seen the development of “total-evidence” analyses, which combine molecular and morphological data from extant and past sampled individuals in a unified Bayesian inference framework. Even sampled individuals characterized only by their sampling time, i.e. lacking morphological and molecular data, which we call occurrences, provide invaluable information to reconstruct past population sizes.Here, we present new methodological developments around the Fossilized Birth-Death Process enabling us to (i) efficiently incorporate occurrence data while remaining computationally tractable and scalable; (ii) consider piecewise-constant birth, death and sampling rates; and (iii) reconstruct past population sizes, with or without knowledge of the underlying tree. We implement our method in the RevBayes software environment, enabling its use along with a large set of models of molecular and morphological evolution, and validate the inference workflow using simulations under a wide range of conditions.We finally illustrate our new implementation using two empirical datasets stemming from the fields of epidemiology and macroevolution. In epidemiology, we apply our model to the Covid-19 outbreak on the Diamond Princess ship. We infer the total prevalence throughout the outbreak, by taking into account jointly the case count record (occurrences) along with viral sequences for a fraction of infected individuals. In macroevolution, we present an empirical case study of cetaceans. We infer the diversity trajectory using molecular and morphological data from extant taxa, morphological data from fossils, as well as numerous fossil occurrences. Our case studies highlight that the advances we present allow us to further bridge the gap between between epidemiology and pathogen genomics, as well as paleontology and molecular phylogenetics.

TOTAL-EVIDENCE BAYESIAN INFERENCE OF PAST DIVERSITY: THE OCCURRENCE BIRTH-DEATH PROCESS

2020 ◽  
Author(s):  
Jérémy Andréoletti ◽  
◽  
Antoine Zwaans ◽  
Antoine Zwaans ◽  
Rachel C.M. Warnock ◽  
...  
Keyword(s):  
Bayesian Inference ◽  
Total Evidence ◽  
Death Process ◽  
Birth Death

scholarly journals Impacts of Taxon-Sampling Schemes on Bayesian Molecular Dating under the Unresolved Fossilized Birth-Death Process

2021 ◽  
Author(s):  
Arong Luo ◽  
Chi Zhang ◽  
Qing-Song Zhou ◽  
Simon Y.W. Ho ◽  
Chao-Dong Zhu
Keyword(s):  
Molecular Dating ◽  
Total Evidence ◽  
Death Process ◽  
Taxon Sampling ◽  
Data Set ◽  
Sampling Density ◽  
Sampling Schemes ◽  
Divergence Time Estimates ◽  
Tree Topologies ◽  
Birth Death

Evolutionary timescales can be estimated using a combination of genetic data and fossil evidence based on the molecular clock. Bayesian phylogenetic methods such as tip dating and total-evidence dating provide a powerful framework for inferring evolutionary timescales, but the most widely used priors for tree topologies and node times often assume that present-day taxa have been sampled randomly or exhaustively. In practice, taxon sampling is often carried out so as to include representatives of major lineages, such as orders or families. We examined the impacts of these diversified sampling schemes on Bayesian molecular dating under the unresolved fossilized birth-death (FBD) process, in which fossil taxa are topologically constrained but their exact placements are not inferred. We used synthetic data generated by simulation of nucleotide sequence evolution, fossil occurrences, and diversified taxon sampling. Our analyses show that increasing sampling density does not substantially improve divergence-time estimates under benign conditions. However, when the tree topologies were fixed to those used for simulation or when evolutionary rates varied among lineages, the performance of Bayesian tip dating improves with sampling density. By exploring three situations of model mismatches, we find that including all relevant fossils without pruning off those inappropriate for the FBD process can lead to underestimation of divergence times. Our reanalysis of a eutherian mammal data set confirms some of the findings from our simulation study, and reveals the complexity of diversified taxon sampling in phylogenomic data sets. In highlighting the interplay of taxon-sampling density and other factors, the results of our study have useful implications for Bayesian molecular dating in the era of phylogenomics.

scholarly journals Total-Evidence Dating under the Fossilized Birth–Death Process

2015 ◽  
Vol 65 (2) ◽  
pp. 228-249 ◽  
Author(s):  
Chi Zhang ◽  
Tanja Stadler ◽  
Seraina Klopfstein ◽  
Tracy A. Heath ◽  
Fredrik Ronquist
Keyword(s):  
Total Evidence ◽  
Death Process ◽  
Birth Death

scholarly journals Estimating the age of poorly dated fossil specimens and deposits using a total-evidence approach and the fossilized birth-death process

2021 ◽  
Author(s):  
Joelle Barido-Sottani ◽  
Dagmara Zyla ◽  
Tracy A. Heath
Keyword(s):  
Phylogenetic Analysis ◽  
Fossil Record ◽  
Phylogenetic Analyses ◽  
Total Evidence ◽  
Baltic Amber ◽  
Death Process ◽  
Gobi Desert ◽  
The Baltic ◽  
Age Estimates ◽  
Birth Death

Bayesian total-evidence approaches under the fossilized birth-death model enable biologists to combine fossil and extant data---while accounting for uncertainty in the ages of fossil specimens---in an integrative phylogenetic analysis. Fossil age uncertainty is a key feature of the fossil record as many empirical datasets may contain a mix of precisely dated and poorly dated fossil specimens or deposits. In this study, we explore whether reliable age estimates for fossil specimens can be obtained from Bayesian total-evidence phylogenetic analyses under the fossilized birth-death model. Through simulations based on the example of the Baltic amber deposit, we show that estimates of fossil ages obtained through such an analysis are accurate, particularly when the proportion of poorly dated specimens remains low and the majority of fossil specimens have precise dates. We confirm our results using an empirical dataset of living and fossil penguins by artificially increasing the age uncertainty around some fossil specimens and showing that the resulting age estimates overlap with the recorded age ranges. Our results are applicable to many empirical datasets where classical methods of establishing fossil ages have failed, such as the Baltic amber and the Gobi Desert deposits.

Normal approximations to discrete unimodal distributions

1986 ◽  
Vol 23 (04) ◽  
pp. 1013-1018
Author(s):  
B. G. Quinn ◽  
H. L. MacGillivray
Keyword(s):  
Stationary Distribution ◽  
Sufficient Conditions ◽  
Random Variables ◽  
Hypergeometric Distribution ◽  
Death Process ◽  
Normal Approximations ◽  
Discrete Random Variables ◽  
Birth Death

Sufficient conditions are presented for the limiting normality of sequences of discrete random variables possessing unimodal distributions. The conditions are applied to obtain normal approximations directly for the hypergeometric distribution and the stationary distribution of a special birth-death process.

A new species of Contomastix (Squamata, Teiidae) supported by total evidence, with remarks on diagnostic characters defining the genus

2019 ◽  
pp. 23-36
Author(s):  
Mario. R. Cabrera
Keyword(s):  
New Species ◽  
Geographic Distribution ◽  
Phylogenetic Reconstruction ◽  
Total Evidence ◽  
Molecular Evidence ◽  
Proximal Margin ◽  
Diagnostic Characters ◽  
Morphological Differences ◽  
A New Species ◽  
Molecular Characters

Formerly Cnemidophorus was thought to be the most speciose genus of Teiidae. This genus comprised four morphological groups that were later defined as four different genera, Ameivula, Aurivela, Cnemidophorus and Contomastix. The last appears as paraphyletic in a recent phylogenetic reconstruction based on morphology, but monophyletic in a reconstruction using molecular characters. Six species are allocated to Contomastix. One of them, C. lacertoides, having an extensive and disjunct geographic distribution in Argentina, Uruguay and Brazil. Preliminary analyses revealed morphological differences among its populations, suggesting that it is actually a complex of species. Here, we describe a new species corresponding to the Argentinian populations hitherto regarded as C. lacertoides, by integrating morphological and molecular evidence. Furthermore, we demonstrate that the presence of notched proximal margin of the tongue is a character that defines the genus Contomastix.

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