The fossilized birth-death process for coherent calibration of divergence-time estimates

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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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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Molecular phylogeny and divergence time estimates of Penaeid Shrimp Lineages (Decapoda: Penaeidae)

Zootaxa ◽

10.11646/zootaxa.2107.1.2 ◽

2009 ◽

Vol 2107 (1) ◽

pp. 41-52 ◽

Cited By ~ 5

Author(s):

CAROLINA M VOLOCH ◽

PABLO R FREIRE ◽

CLAUDIA A M RUSSO

Keyword(s):

Fossil Record ◽

Divergence Time ◽

Penaeid Shrimp ◽

Divergence Time Estimates ◽

Time Estimates ◽

Global Clock ◽

Late Tertiary ◽

The Family ◽

Molecular Studies ◽

Triassic Period

Fossil record of penaeids indicates that the family exists since the Triassic period, but extant genera appeared only recently in Tertiary strata. Molecular based divergence time estimates on the matter of penaeid radiation were never properly addressed, due to shortcomings of the global molecular clock assumptions. Here, we studied the diversification patterns of the family, uncovering, more specifically, a correlation between fossil and extant Penaeid fauna. For this, we have used a Bayesian framework that does not assume a global clock. Our results suggest that Penaeid genera originated between 20 million years ago and 43 million years ago, much earlier than expected by previous molecular studies. Altogether, these results promptly discard late Tertiary or even Quaternary hypotheses that presumed a major glaciations influence on the diversification patterns of the family.

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Out of the Neotropics: Late Cretaceous colonization of Australasia by American arthropods

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2012.0675 ◽

2012 ◽

Vol 279 (1742) ◽

pp. 3501-3509 ◽

Cited By ~ 41

Author(s):

Prashant P. Sharma ◽

Gonzalo Giribet

Keyword(s):

Late Cretaceous ◽

Divergence Time ◽

Disjunct Distribution ◽

Continental Margins ◽

Divergence Time Estimates ◽

Evolutionary Origins ◽

Source Regions ◽

Time Estimates ◽

Fiji Islands ◽

The Pacific

The origins of tropical southwest Pacific diversity are traditionally attributed to southeast Asia or Australia. Oceanic and fragment islands are typically colonized by lineages from adjacent continental margins, resulting in attrition of diversity with distance from the mainland. Here, we show that an exceptional tropical family of harvestmen with a trans-Pacific disjunct distribution has its origin in the Neotropics. We found in a multi-locus phylogenetic analysis that the opilionid family Zalmoxidae, which is distributed in tropical forests on both sides of the Pacific, is a monophyletic entity with basal lineages endemic to Amazonia and Mesoamerica. Indo-Pacific Zalmoxidae constitute a nested clade, indicating a single colonization event. Lineages endemic to putative source regions, including Australia and New Guinea, constitute derived groups. Divergence time estimates and probabilistic ancestral area reconstructions support a Neotropical origin of the group, and a Late Cretaceous ( ca 82 Ma) colonization of Australasia out of the Fiji Islands and/or Borneo, which are consistent with a transoceanic dispersal event. Our results suggest that the endemic diversity within traditionally defined zoogeographic boundaries might have more complex evolutionary origins than previously envisioned.

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Phylogenetic relationships and divergence time estimates in the genus Echinops L. (Asteraceae)

Nordic Journal of Botany ◽

10.1111/njb.03081 ◽

2021 ◽

Vol 39 (3) ◽

Author(s):

Handan Şapci Selamoğlu

Keyword(s):

Phylogenetic Relationships ◽

Divergence Time ◽

Divergence Time Estimates ◽

Time Estimates

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Using a GTR+Γ substitution model for dating sequence divergence when stationarity and time-reversibility assumptions are violated

Bioinformatics ◽

10.1093/bioinformatics/btaa820 ◽

2020 ◽

Vol 36 (Supplement_2) ◽

pp. i884-i894

Author(s):

Jose Barba-Montoya ◽

Qiqing Tao ◽

Sudhir Kumar

Keyword(s):

Divergence Time ◽

Sequence Divergence ◽

Molecular Dating ◽

Divergence Times ◽

Time Reversibility ◽

Sequence Alignments ◽

Divergence Time Estimates ◽

Time Estimates ◽

Substitution Process ◽

The Impact

Abstract Motivation As the number and diversity of species and genes grow in contemporary datasets, two common assumptions made in all molecular dating methods, namely the time-reversibility and stationarity of the substitution process, become untenable. No software tools for molecular dating allow researchers to relax these two assumptions in their data analyses. Frequently the same General Time Reversible (GTR) model across lineages along with a gamma (+Γ) distributed rates across sites is used in relaxed clock analyses, which assumes time-reversibility and stationarity of the substitution process. Many reports have quantified the impact of violations of these underlying assumptions on molecular phylogeny, but none have systematically analyzed their impact on divergence time estimates. Results We quantified the bias on time estimates that resulted from using the GTR + Γ model for the analysis of computer-simulated nucleotide sequence alignments that were evolved with non-stationary (NS) and non-reversible (NR) substitution models. We tested Bayesian and RelTime approaches that do not require a molecular clock for estimating divergence times. Divergence times obtained using a GTR + Γ model differed only slightly (∼3% on average) from the expected times for NR datasets, but the difference was larger for NS datasets (∼10% on average). The use of only a few calibrations reduced these biases considerably (∼5%). Confidence and credibility intervals from GTR + Γ analysis usually contained correct times. Therefore, the bias introduced by the use of the GTR + Γ model to analyze datasets, in which the time-reversibility and stationarity assumptions are violated, is likely not large and can be reduced by applying multiple calibrations. Availability and implementation All datasets are deposited in Figshare: https://doi.org/10.6084/m9.figshare.12594638.

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Relaxed Clocks and Inferences of Heterogeneous Patterns of Nucleotide Substitution and Divergence Time Estimates across Whales and Dolphins (Mammalia: Cetacea)

Molecular Biology and Evolution ◽

10.1093/molbev/msr228 ◽

2011 ◽

Vol 29 (2) ◽

pp. 721-736 ◽

Cited By ~ 85

Author(s):

A. Dornburg ◽

M. C. Brandley ◽

M. R. McGowen ◽

T. J. Near

Keyword(s):

Nucleotide Substitution ◽

Divergence Time ◽

Divergence Time Estimates ◽

Time Estimates

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Morphological and molecular phylogenetic analyses of Zepedanulus ishikawai (Arachnida: Opiliones: Laniatores: Epedanidae) in the southern part of the Ryukyu Archipelago

The Canadian Entomologist ◽

10.4039/tce.2021.42 ◽

2021 ◽

pp. 1-28

Author(s):

Yoshimasa Kumekawa ◽

Haruka Fujimoto ◽

Osamu Miura ◽

Ryo Arakawa ◽

Jun Yokoyama ◽

...

Keyword(s):

Phylogenetic Tree ◽

Phylogenetic Analyses ◽

Divergence Time ◽

Morphological Characters ◽

Ryukyu Archipelago ◽

Divergence Time Estimates ◽

Time Estimates ◽

Molecular Phylogenetic ◽

History Of ◽

Polymerase Chain

Abstract Harvestmen (Arachnida: Opiliones) are soil animals with extremely low dispersal abilities that experienced allopatric differentiation. To clarify the morphological and phylogenetic differentiation of the endemic harvestman Zepedanulus ishikawai (Suzuki, 1971) (Laniatores: Epedanidae) in the southern part of the Ryukyu Archipelago, we conducted molecular phylogenetic analyses and divergence time estimates based on CO1 and 16S rRNA sequences of mtDNA, the 28S rRNA sequence of nrDNA, and the external morphology. A phylogenetic tree based on mtDNA sequences indicated that individuals of Z. ishikawai were monophyletic and were divided into clade I and clade II. This was supported by the nrDNA phylogenetic tree. Although clades I and II were distributed sympatrically on all three islands examined (Ishigaki, Iriomote, and Yonaguni), heterogeneity could not be detected by polymerase chain reaction–restriction fragment length polymorphism of nrDNA, indicating that clades I and II do not have a history of hybridisation. Also, several morphological characters differed significantly between individuals of clade I and clade II. The longstanding isolation of the southern Ryukyus from the surrounding islands enabled estimation of the original morphological characters of both clades of Z. ishikawai.

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Uncertainty in divergence time estimation

Systematic Biology ◽

10.1093/sysbio/syaa096 ◽

2020 ◽

Author(s):

Tom Carruthers ◽

Robert W Scotland

Keyword(s):

Fossil Record ◽

Academic Research ◽

Divergence Time ◽

Time Estimation ◽

Divergence Time Estimation ◽

Diversification Rates ◽

Divergence Time Estimates ◽

Use Of Time ◽

Time Estimates ◽

Highly Sensitive

Abstract Understanding and representing uncertainty is crucial in academic research, because it enables studies to build on the conclusions of previous studies, leading to robust advances in a particular field. Here, we evaluate the nature of uncertainty and the manner by which it is represented in divergence time estimation, a field that is fundamental to many aspects of macroevolutionary research, and where there is evidence that uncertainty has been seriously underestimated. We address this issue in the context of methods used in divergence time estimation, and with respect to the manner by which time-calibrated phylogenies are interpreted. With respect to methods, we discuss how the assumptions underlying different methods may not adequately reflect uncertainty about molecular evolution, the fossil record, or diversification rates. Therefore, divergence time estimates may not adequately reflect uncertainty, and may be directly contradicted by subsequent findings. For the interpretation of time-calibrated phylogenies, we discuss how the use of time-calibrated phylogenies for reconstructing general evolutionary timescales leads to inferences about macroevolution that are highly sensitive to methodological limitations in how uncertainty is accounted for. By contrast, we discuss how the use of time-calibrated phylogenies to test specific hypotheses leads to inferences about macroevolution that are less sensitive to methodological limitations. Given that many biologists wish to use time-calibrated phylogenies to reconstruct general evolutionary timescales, we conclude that the development of methods of divergence time estimation that adequately account for uncertainty is necessary.

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