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

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.

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The taxonomic placement of three fossil Fundulus species and the timing of divergence within the North American topminnows (Teleostei: Fundulidae)

Zootaxa ◽

10.11646/zootaxa.4250.6.5 ◽

2017 ◽

Vol 4250 (6) ◽

pp. 577 ◽

Cited By ~ 5

Author(s):

MICHAEL J. GHEDOTTI ◽

MATTHEW P. DAVIS

Keyword(s):

Sequence Data ◽

Divergence Time ◽

Time Estimation ◽

Species Group ◽

Total Evidence ◽

Morphological Data ◽

Fossil Species ◽

Divergence Time Estimation ◽

Biogeographic History ◽

Extant Species

The fossils species †Fundulus detillae, †F. lariversi, and †F. nevadensis from localities in the western United States are represented by well-preserved material with date estimations. We combined morphological data for these fossil taxa with morphological and DNA-sequence data to conduct a phylogenetic analysis and a tip-based divergence-time estimation for the family Fundulidae. The resultant phylogeny is largely concordant with the prior total-evidence phylogeny. The fossil species do not form a monophyletic group, and do not represent a discrete western radiation of Fundulus as previously proposed. The genus Fundulus diverged into subgeneric clades likely in the Eocene or Oligocene (mean age 34.6 mya, 53–23 mya), and all subgeneric and most species-group clades had evolved by the middle Miocene. †Fundulus lariversi is a member of subgenus Fundulus in which all extant species are found only in eastern North America, demonstrating that fundulids had a complicated biogeographic history. We confirmed †Fundulus detillae as a member of the subgenus Plancterus. †F. nevadensis is not classified in a subgenus but likely is related to the subgenera Plancterus and Wileyichthys.

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Genetic Differentiation and Divergence Time of Chinese Parnassius (Lepidoptera: Papilionidae) Species Based on Nuclear Internal Transcribed Spacer (ITS) Sequence Data

Journal of Entomological Science ◽

10.18474/0749-8004-55.4.520 ◽

2020 ◽

Vol 55 (4) ◽

pp. 520-546

Author(s):

Chengcai Si ◽

Keke Chen ◽

Ruisong Tao ◽

Chengyong Su ◽

Junye Ma ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Genetic Differentiation ◽

Species Identification ◽

Internal Transcribed Spacer ◽

Sequence Data ◽

Divergence Time ◽

Time Estimation ◽

Western China ◽

Tibet Plateau ◽

Divergence Time Estimation

Abstract Parnassius (Lepidoptera: Papilionidae) is a genus of attractive butterflies mainly distributed in the mountainous areas of Central Asia, the Himalayas, and western China. In this study, we used the internal transcribed spacer (ITS1 and ITS2) sequence data as DNA barcodes to characterize the genetic differentiation and conduct the phylogenetic analysis and divergence time estimation of the 17 Parnassius species collected in China. Species identification and genetic differentiation analysis suggest that the ITS barcode is an effective marker for Parnassius species identification; additionally, a relatively high level of genetic diversity and low level of gene flow were detected in the five Parnassius species with diverse geographic populations. Phylogenetic analysis indicates that the 17 species studied were clustered in six clades (subgenera), with subgenus Parnassius at the basal position in the phylogenetic trees. Bayesian divergence time estimation shows that the genus originated about 18 million years ago during the early Miocene, correlated with orogenic events in the distribution region, probably southwestern China about 20–10 million years ago. Our estimated phylochronology also suggests that the Parnassius interspecific and intraspecific divergences were probably related with the rapid rising of the Qinghai-Tibet Plateau, the Tibet Movement, the Kunlun-Yellow River Tectonic Movement, and global cooling associated with intensified glaciation in the region during the Quaternary Period.

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Using Phylogenomic Data to Explore the Effects of Relaxed Clocks and Calibration Strategies on Divergence Time Estimation: Primates as a Test Case

10.1101/201327 ◽

2017 ◽

Cited By ~ 1

Author(s):

Mario dos Reis ◽

Gregg F. Gunnell ◽

José Barba-Montoya ◽

Alex Wilkins ◽

Ziheng Yang ◽

...

Keyword(s):

Sequence Data ◽

Divergence Time ◽

Time Estimation ◽

Test Case ◽

Base Pairs ◽

Molecular Sequence Data ◽

Divergence Time Estimation ◽

Divergence Time Estimates ◽

Time Estimates ◽

Clock Models

AbstractPrimates have long been a test case for the development of phylogenetic methods for divergence time estimation. Despite a large number of studies, however, the timing of origination of crown Primates relative to the K-Pg boundary and the timing of diversification of the main crown groups remain controversial. Here we analysed a dataset of 372 taxa (367 Primates and 5 outgroups, 61 thousand base pairs) that includes nine complete primate genomes (3.4 million base pairs). We systematically explore the effect of different interpretations of fossil calibrations and molecular clock models on primate divergence time estimates. We find that even small differences in the construction of fossil calibrations can have a noticeable impact on estimated divergence times, especially for the oldest nodes in the tree. Notably, choice of molecular rate model (auto-correlated or independently distributed rates) has an especially strong effect on estimated times, with the independent rates model producing considerably more ancient estimates for the deeper nodes in the phylogeny. We implement thermodynamic integration, combined with Gaussian quadrature, in the program MCMCTree, and use it to calculate Bayes factors for clock models. Bayesian model selection indicates that the auto-correlated rates model fits the primate data substantially better, and we conclude that time estimates under this model should be preferred. We show that for eight core nodes in the phylogeny, uncertainty in time estimates is close to the theoretical limit imposed by fossil uncertainties. Thus, these estimates are unlikely to be improved by collecting additional molecular sequence data. All analyses place the origin of Primates close to the K-Pg boundary, either in the Cretaceous or straddling the boundary into the Palaeogene.

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Inferring the Total-Evidence Timescale of Marattialean Fern Evolution in the Face of Model Sensitivity

10.1101/2020.09.25.313643 ◽

2020 ◽

Author(s):

Michael R. May ◽

Dori L. Contreras ◽

Michael A. Sundue ◽

Nathalie S. Nagalingum ◽

Cindy V. Looy ◽

...

Keyword(s):

Morphological Evolution ◽

Divergence Time ◽

Time Estimation ◽

Bayes Factors ◽

Total Evidence ◽

Rate Variation ◽

Divergence Time Estimation ◽

Extinction Rates ◽

Extant Species ◽

Tree Models

AbstractPhylogenetic divergence-time estimation has been revolutionized by two recent developments: 1) total-evidence dating (or “tip-dating”) approaches that allow for the incorporation of fossils as tips in the analysis, with their phylogenetic and temporal relationships to the extant taxa inferred from the data, and 2) the fossilized birth-death (FBD) class of tree models that capture the processes that produce the tree (speciation, extinction, and fossilization), and thus provide a coherent and biologically interpretable tree prior. To explore the behaviour of these methods, we apply them to marattialean ferns, a group that was dominant in Carboniferous landscapes prior to declining to its modest extant diversity of slightly over 100 species. We show that tree models have a dramatic influence on estimates of both divergence times and topological relationships. This influence is driven by the strong, counter-intuitive informativeness of the uniform tree prior and the inherent nonidentifiability of divergence-time models. In contrast to the strong influence of the tree models, we find minor effects of differing the morphological transition model or the morphological clock model. We compare the performance of a large pool of candidate models using a combination of posterior-predictive simulation and Bayes factors. Notably, an FBD model with epoch-specific speciation and extinction rates was strongly favored by Bayes factors. Our best-fitting model infers stem and crown divergences for the Marattiales in the Middle Devonian and Upper Cretaceous, respectively, with elevated speciation rates in the Mississippian and elevated extinction rates in the Cisuralian leading to a peak diversity of ∼2800 species at the end of the Carboniferous, representing the heyday of the Psaroniaceae. This peak is followed by the rapid decline and ultimate extinction of the Psaroniaceae, with their descendants, the Marattiaceae, persisting at approximately stable levels of diversity until the present. This general diversification pattern appears to be insensitive to potential biases in the fossil record; despite the preponderance of available fossils being from Pennsylvanian coal balls, incorporating fossilization-rate variation does not improve model fit. In addition, by incorporating temporal data directly within the model and allowing for the inference of the phylogenetic position of the fossils, our study makes the surprising inference that the clade of extant Marattiales is relatively young, younger than any of the fossils historically thought to be congeneric with extant species. This result is a dramatic demonstration of the dangers of node-based approaches to divergence-time estimation, where the assignment of fossils to particular clades are made a priori (earlier node-based studies that constrained the minimum ages of extant genera based on these fossils resulted in much older age estimates than in our study) and of the utility of explicit models of morphological evolution and lineage diversification.

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MCMCtreeR: functions to prepare MCMCtree analyses and visualize posterior ages on trees

Bioinformatics ◽

10.1093/bioinformatics/btz554 ◽

2019 ◽

Cited By ~ 5

Author(s):

Mark N Puttick

Keyword(s):

Divergence Time ◽

Time Estimation ◽

R Package ◽

Posterior Distributions ◽

Time Analysis ◽

Divergence Time Estimation ◽

R Packages ◽

Geological Timescale ◽

Time Information ◽

Age Estimates

Abstract Summary The fossil record is incomplete, so molecular divergence time analysis is a crucial tool in estimating evolutionary timescales. MCMCtree contained in the PAML software provides Bayesian methods to estimate divergence times of genomic-sized sequences. Here, I present MCMCtreeR, a flexible R package to prepare time priors for MCMCtree analysis and plot time-scaled phylogenies. The package provides functions to refine parameters and visualize time-calibrated node prior distributions so that these priors accurately reflect confidence in known, usually fossil, time information. After the parameters have been chosen, the package produces output files ready for MCMCtree analysis. Following analysis, the package has tools to compare prior and posterior calibrated node age distributions and produce plots of the time-scaled phylogenies. The plotting functions allow for the inclusion of age uncertainty on time-scaled phylogenies, including the display of full posterior distributions on nodes. Options also allow for the inclusion of the geological timescale, and these plotting functions are applicable with posterior age estimates from any Bayesian divergence time estimation software. Availability and implementation MCMCtreeR is an R package available on CRAN (https://CRAN.R-project.org/package=MCMCtreeR). MCMCtreeR depends on the R packages ape, sn and stats4.

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Ignoring stratigraphic age uncertainty leads to erroneous estimates of species divergence times under the fossilized birth-death process

10.1101/477133 ◽

2018 ◽

Cited By ~ 1

Author(s):

Joëlle Barido-Sottani ◽

Gabriel Aguirre-Fernández ◽

Melanie Hopkins ◽

Tanja Stadler ◽

Rachel Warnock

Keyword(s):

Divergence Time ◽

Time Estimation ◽

Death Process ◽

Divergence Times ◽

Point Estimate ◽

Species Divergence ◽

Divergence Time Estimation ◽

Divergence Time Estimates ◽

Time Estimates ◽

Birth Death

AbstractFossil information is essential for estimating species divergence times, and can be integrated into Bayesian phylogenetic inference using the fossilized birth-death (FBD) process. An important aspect of palaeontological data is the uncertainty surrounding specimen ages, which can be handled in different ways during inference. The most common approach is to fix fossil ages to a point estimate within the known age interval. Alternatively, age uncertainty can be incorporated by using priors, and fossil ages are then directly sampled as part of the inference. This study presents a comparison of alternative approaches for handling fossil age uncertainty in analysis using the FBD process. Based on simulations, we find that fixing fossil ages to the midpoint or a random point drawn from within the stratigraphic age range leads to biases in divergence time estimates, while sampling fossil ages leads to estimates that are similar to inferences that employ the correct ages of fossils. Second, we show a comparison using an empirical dataset of extant and fossil cetaceans, which confirms that different methods of handling fossil age uncertainty lead to large differences in estimated node ages. Stratigraphic age uncertainty should thus not be ignored in divergence time estimation and instead should be incorporated explicitly.

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Divergence times in demosponges (Porifera): first insights from new mitogenomes and the inclusion of fossils in a birth-death clock model

10.1101/159806 ◽

2017 ◽

Cited By ~ 4

Author(s):

Astrid Schuster ◽

Sergio Vargas ◽

Ingrid S. Knapp ◽

Shirley A. Pomponi ◽

Robert J. Toonen ◽

...

Keyword(s):

Sequence Data ◽

Divergence Time ◽

Marine Sponges ◽

Divergence Times ◽

Mitochondrial Genomes ◽

Freshwater Sponges ◽

Molecular Sequence Data ◽

Genomic Libraries ◽

Age Estimates ◽

Birth Death

AbstractApproximately 80% of all recent sponge species belong to the class Demospongiae. Yet, despite their diversity and importance, accurate divergence times are still unknown for most demosponge clades. The estimation of demosponge divergence time is key to answering fundamental questions like e.g. the origin of Demospongiae, their diversification and historical biogeography. Molecular sequence data alone is not informative on an absolute time scale, and therefore needs to be “calibrated” with additional data such as fossils. Here, we apply the fossilized birth-death model (FBD), which has the advantage, compared to strict node dating with the oldest fossil occurrences, that it allows for the inclusion of young and old fossils in the analysis of divergence time. We use desma-bearing sponges, a diverse group of demosponges that form rigid skeletons and have a rich and continuous fossil record dating back to the Cambrian (∼500 Ma), aiming to date the demosponge radiation and constrain the timing of key evolutionary events, like the transition from marine to freshwater habitats. To do so, we assembled mitochondrial genomes of six desma-bearing demosponges from size-selected reduced-representation genomic libraries and apply a fossilized birth-death model including 30 fossils and 33 complete demosponge mitochondrial genomes to infer a dated phylogeny of Demospongiae. Our study supports a Neoproterozoic origin of Demospongiae. Novel age estimates for the split of freshwater and marine sponges dating back to the Carboniferous and the previously assumed Recent (∼18 Ma) diversification of freshwater sponges is supported. Moreover, we provide detailed age estimates for a possible diversification of Tetractinellidae (∼315 Ma), the Astrophorina (∼240 Ma), the Spirophorina (∼120 Ma) and the family Corallistidae (∼188 Ma) all of which are considered as key groups for dating the Demospongiae, due to their extraordinary rich and continuous fossil history.

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Ignoring stratigraphic age uncertainty leads to erroneous estimates of species divergence times under the fossilized birth–death process

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2019.0685 ◽

2019 ◽

Vol 286 (1902) ◽

pp. 20190685 ◽

Cited By ~ 14

Author(s):

Joëlle Barido-Sottani ◽

Gabriel Aguirre-Fernández ◽

Melanie J. Hopkins ◽

Tanja Stadler ◽

Rachel Warnock

Keyword(s):

Divergence Time ◽

Time Estimation ◽

Death Process ◽

Divergence Times ◽

Point Estimate ◽

Species Divergence ◽

Divergence Time Estimation ◽

Divergence Time Estimates ◽

Time Estimates ◽

Birth Death

Fossil information is essential for estimating species divergence times, and can be integrated into Bayesian phylogenetic inference using the fossilized birth–death (FBD) process. An important aspect of palaeontological data is the uncertainty surrounding specimen ages, which can be handled in different ways during inference. The most common approach is to fix fossil ages to a point estimate within the known age interval. Alternatively, age uncertainty can be incorporated by using priors, and fossil ages are then directly sampled as part of the inference. This study presents a comparison of alternative approaches for handling fossil age uncertainty in analysis using the FBD process. Based on simulations, we find that fixing fossil ages to the midpoint or a random point drawn from within the stratigraphic age range leads to biases in divergence time estimates, while sampling fossil ages leads to estimates that are similar to inferences that employ the correct ages of fossils. Second, we show a comparison using an empirical dataset of extant and fossil cetaceans, which confirms that different methods of handling fossil age uncertainty lead to large differences in estimated node ages. Stratigraphic age uncertainty should thus not be ignored in divergence time estimation and instead should be incorporated explicitly.

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Assessing the quality of molecular divergence time estimates by fossil calibrations and fossil–based model selection

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2004.1523 ◽

2004 ◽

Vol 359 (1450) ◽

pp. 1477-1483 ◽

Cited By ~ 126

Author(s):

Thomas J. Near ◽

Michael J. Sanderson

Keyword(s):

Cross Validation ◽

Sequence Data ◽

Divergence Time ◽

Evolutionary Model ◽

Time Estimation ◽

Optimal Estimation ◽

Divergence Time Estimation ◽

Fossil Calibration ◽

Divergence Time Estimates ◽

The Impact

Estimates of species divergence times using DNA sequence data are playing an increasingly important role in studies of evolution, ecology and biogeography. Most work has centred on obtaining appropriate kinds of data and developing optimal estimation procedures, whereas somewhat less attention has focused on the calibration of divergences using fossils. Case studies with multiple fossil calibration points provide important opportunities to examine the divergence time estimation problem in new ways. We discuss two cross–validation procedures that address different aspects of inference in divergence time estimation. ‘Fossil cross–validation’ is a procedure used to identify the impact of different individual calibrations on overall estimation. This can identify fossils that have an exceptionally large error effect and may warrant further scrutiny. ‘Fossil–based model cross–validation’ is an entirely different procedure that uses fossils to identify the optimal model of molecular evolution in the context of rate smoothing or other inference methods. Both procedures were applied to two recent studies: an analysis of monocot angiosperms with eight fossil calibrations and an analysis of placental mammals with nine fossil calibrations. In each case, fossil calibrations could be ranked from most to least influential, and in one of the two studies, the fossils provided decisive evidence about the optimal molecular evolutionary model.

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Ebony and the Mascarenes: the evolutionary relationships and biogeography of Diospyros (Ebenaceae) in the western Indian Ocean

Botanical Journal of the Linnean Society ◽

10.1093/botlinnean/boz034 ◽

2019 ◽

Vol 190 (4) ◽

pp. 359-373 ◽

Cited By ~ 5

Author(s):

Alexander G Linan ◽

George E Schatz ◽

Porter P Lowry ◽

Allison Miller ◽

Christine E Edwards

Keyword(s):

Sequence Data ◽

Phylogenetic Analyses ◽

Divergence Time ◽

Time Estimation ◽

Western Indian Ocean ◽

Evolutionary Relationships ◽

Ancestral Area ◽

Molecular Analyses ◽

Divergence Time Estimation ◽

Mascarene Islands

Abstract Using analyses that exhaustively sampled Mascarene Diospyros and included representative taxa from Madagascar and other regions, we explored: (1) evolutionary relationships among Diospyros spp. across the WIO and (2) biogeographic connections of Malagasy taxa with those in surrounding regions, particularly focusing on connections with taxa in the Mascarene Islands. We obtained plastid sequence data for 146 Diospyros taxa, including 40 species not previously included in molecular analyses, and conducted Bayesian and maximum-likelihood phylogenetic analyses, divergence-time estimation and ancestral area reconstructions. Diospyros sampled from Madagascar fell into two clades, one of which contains all but two Malagasy species. Biogeographic analyses revealed that many clades probably originated in Madagascar and dispersed to locations in Africa and the Mascarenes, indicating that Madagascar may have acted as an important source of diversity for the region.

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