Uncertainty in divergence time estimation

Diversification Rates ◽

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.

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 ◽

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 ◽

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.

The Implications of Lineage-Specific Rates for Divergence Time Estimation

Systematic Biology ◽

10.1093/sysbio/syz080 ◽

2019 ◽

Vol 69 (4) ◽

pp. 660-670 ◽

Author(s):

Tom Carruthers ◽

Michael J Sanderson ◽

Robert W Scotland

Keyword(s):

Estimation Error ◽

Divergence Time ◽

Time Estimation ◽

Rate Variation ◽

Data Set ◽

Time Estimates ◽

The Impact ◽

Highest Posterior Density

Abstract Rate variation adds considerable complexity to divergence time estimation in molecular phylogenies. Here, we evaluate the impact of lineage-specific rates—which we define as among-branch-rate-variation that acts consistently across the entire genome. We compare its impact to residual rates—defined as among-branch-rate-variation that shows a different pattern of rate variation at each sampled locus, and gene-specific rates—defined as variation in the average rate across all branches at each sampled locus. We show that lineage-specific rates lead to erroneous divergence time estimates, regardless of how many loci are sampled. Further, we show that stronger lineage-specific rates lead to increasing error. This contrasts to residual rates and gene-specific rates, where sampling more loci significantly reduces error. If divergence times are inferred in a Bayesian framework, we highlight that error caused by lineage-specific rates significantly reduces the probability that the 95% highest posterior density includes the correct value, and leads to sensitivity to the prior. Use of a more complex rate prior—which has recently been proposed to model rate variation more accurately—does not affect these conclusions. Finally, we show that the scale of lineage-specific rates used in our simulation experiments is comparable to that of an empirical data set for the angiosperm genus Ipomoea. Taken together, our findings demonstrate that lineage-specific rates cause error in divergence time estimates, and that this error is not overcome by analyzing genomic scale multilocus data sets. [Divergence time estimation; error; rate variation.]

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

10.1101/477133 ◽

2018 ◽

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 ◽

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.

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 ◽

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.

The Past Sure Is Tense: On Interpreting Phylogenetic Divergence Time Estimates

10.1101/113720 ◽

2017 ◽

Cited By ~ 2

Author(s):

Joseph W. Brown ◽

Stephen A. Smith

Keyword(s):

Bayesian Analysis ◽

Early Cretaceous ◽

Fossil Record ◽

Divergence Time ◽

Time Estimation ◽

Inference Problem ◽

The Impact ◽

Pseudo Data

AbstractDivergence time estimation — the calibration of a phylogeny to geological time — is an integral first step in modelling the tempo of biological evolution (traits and lineages). However, despite increasingly sophisticated methods to infer divergence times from molecular genetic sequences, the estimated age of many nodes across the tree of life contrast significantly and consistently with timeframes conveyed by the fossil record. This is perhaps best exemplified by crown angiosperms, where molecular clock (Triassic) estimates predate the oldest (Early Cretaceous) undisputed angiosperm fossils by tens of millions of years or more. While the incompleteness of the fossil record is a common concern, issues of data limitation and model inadequacy are viable (if underexplored) alternative explanations. In this vein, Beaulieu et al. (2015) convincingly demonstrated how methods of divergence time inference can be misled by both (i) extreme state-dependent molecular substitution rate heterogeneity and (ii) biased sampling of representative major lineages. These results demonstrate the impact of (potentially common) model violations. Here, we suggest another potential challenge: that the configuration of the statistical inference problem (i.e., the parameters, their relationships, and associated priors) alone may preclude the reconstruction of the paleontological timeframe for the crown age of angiosperms. We demonstrate, through sampling from the joint prior (formed by combining the tree (diversification) prior with the calibration densities specified for fossil-calibrated nodes) that with no data present at all, that, an Early Cretaceous crown angiosperms is rejected (i.e., has essentially zero probability). More worrisome, however, is that, for the 24 nodes calibrated by fossils, almost all have indistinguishable marginal prior and posterior age distributions when employing routine lognormal fossil calibration priors. These results indicate that there is inadequate information in the data to overrule the joint prior. Given that these calibrated nodes are strategically placed in disparate regions of the tree, they act to anchor the tree scaffold, and so the posterior inference for the tree as a whole is largely determined by the pseudo-data present in the (often arbitrary) calibration densities. We recommend, as for any Bayesian analysis, that marginal prior and posterior distributions be carefully compared to determine whether signal is coming from the data or prior belief, especially for parameters of direct interest. This recommendation is not novel. However, given how rarely such checks are carried out in evolutionary biology, it bears repeating. Our results demonstrate the fundamental importance of prior/posterior comparisons in any Bayesian analysis, and we hope that they further encourage both researchers and journals to consistently adopt, this crucial step as standard practice. Finally, we note that the results presented here do not refute the biological modelling concerns identified by Beaulieu et al. (2015). Both sets of issues remain apposite to the goals of accurate divergence time estimation, and only by considering them in tandem can we move forward more confidently. [marginal priors; information content; diptych; divergence time estimation; fossil record; BEAST; angiosperms.]

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 ◽

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.

Correction: Large-scale molecular phylogeny, morphology, divergence-time estimation, and the fossil record of advanced caenophidian snakes (Squamata: Serpentes)

PLoS ONE ◽

10.1371/journal.pone.0217959 ◽

2019 ◽

Vol 14 (5) ◽

pp. e0217959 ◽

Author(s):

Hussam Zaher ◽

Robert W. Murphy ◽

Juan Camilo Arredondo ◽

Roberta Graboski ◽

Paulo Roberto Machado-Filho ◽

...

Keyword(s):

Molecular Phylogeny ◽

Fossil Record ◽

Large Scale ◽

Divergence Time ◽

Time Estimation ◽

Divergence Time Estimation

Bees diversified in the age of eudicots

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2012.2686 ◽

2013 ◽

Vol 280 (1755) ◽

pp. 20122686 ◽

Cited By ~ 119

Author(s):

Sophie Cardinal ◽

Bryan N. Danforth

Keyword(s):

Fossil Record ◽

Sequence Data ◽

Close Association ◽

Divergence Time ◽

Dominant Group ◽

Time Estimates ◽

Time Calibration ◽

Angiosperm Species ◽

Almost All

Reliable estimates on the ages of the major bee clades are needed to further understand the evolutionary history of bees and their close association with flowering plants. Divergence times have been estimated for a few groups of bees, but no study has yet provided estimates for all major bee lineages. To date the origin of bees and their major clades, we first perform a phylogenetic analysis of bees including representatives from every extant family, subfamily and almost all tribes, using sequence data from seven genes. We then use this phylogeny to place 14 time calibration points based on information from the fossil record for an uncorrelated relaxed clock divergence time analysis taking into account uncertainties in phylogenetic relationships and the fossil record. We explore the effect of placing a hard upper age bound near the root of the tree and the effect of different topologies on our divergence time estimates. We estimate that crown bees originated approximately 123 Ma (million years ago) (113–132 Ma), concurrently with the origin or diversification of the eudicots, a group comprising 75 per cent of angiosperm species. All of the major bee clades are estimated to have originated during the Middle to Late Cretaceous, which is when angiosperms became the dominant group of land plants.

Fossil Constraints on the Timescale of Parasitic Helminth Evolution

10.32942/osf.io/6jakv ◽

2020 ◽

Author(s):

Kenneth De Baets ◽

Paula Dentzien-Dias ◽

G. William M. Harrison ◽

D. Timothy J. Littlewood ◽

Luke A. Parry

Keyword(s):

Fossil Record ◽

Divergence Time ◽

Late Paleozoic ◽

Early Paleozoic ◽

Parasitic Helminths ◽

Time Estimates ◽

Fossil Evidence ◽

Molecular Divergence ◽

Animal Hosts

The fossil record of parasitic helminths is often stated to be severely limited. Many studies have therefore used host constraints to constrain molecular divergence time estimates of helminths. Here we review direct fossil evidence for several of these parasitic lineages belong to various phyla (Acanthocephala, Annelida, Arthropoda, Nematoda, Nematomorpha, Pentastomida, Platyhelminthes). Our compilation shows that the fossil record of soft-bodied helminths is patchy, but more diverse than commonly assumed. The fossil record provides evidence that ectoparasitic helminths (e.g., worm-like pentastomid arthropods) have been around since the early Paleozoic, while endoparasitic helminths (cestodes) arose at least during, or possibly even before the late Paleozoic. Nematode lineages parasitizing terrestrial plant and animal hosts have been in existence at least since the Devonian and Triassic, respectively. All major phyla (Acanthocephala, Annelida, Platyhelminthes. Nematoda, Nematomorpha) had evolved endoparasitic lineages at least since the Mesozoic. Interestingly, although parasitism is considered derived within Metazoa, the oldest evidence for Nematoda and Platyhelminthes includes body fossils of parasitic representatives. Furthermore, the oldest fossil evidence of these parasitic lineages often falls within molecular divergence time estimates based on host co-evolution suggesting the fossil record of helminths themselves might be just as good or at least complementary (and less circular in justification) to calibration based on host associations. Data also provide evidence for obvious host switches or extinctions, which cautions against models of pure co-divergence where use of host calibrations to constrain divergence time estimates may be considered.

Phylogenomic analysis sheds light on the evolutionary pathways towards acoustic communication in Orthoptera

Nature Communications ◽

10.1038/s41467-020-18739-4 ◽

2020 ◽

Vol 11 (1) ◽

Author(s):

Hojun Song ◽

Olivier Béthoux ◽

Seunggwan Shin ◽

Alexander Donath ◽

Harald Letsch ◽

...

Keyword(s):

Acoustic Communication ◽

Large Scale ◽

Sound Production ◽

Divergence Time ◽

Phylogenomic Analysis ◽

Diversification Rates ◽

Insect Order ◽

Time Estimates ◽

Sexual Signalling

Abstract Acoustic communication is enabled by the evolution of specialised hearing and sound producing organs. In this study, we performed a large-scale macroevolutionary study to understand how both hearing and sound production evolved and affected diversification in the insect order Orthoptera, which includes many familiar singing insects, such as crickets, katydids, and grasshoppers. Using phylogenomic data, we firmly establish phylogenetic relationships among the major lineages and divergence time estimates within Orthoptera, as well as the lineage-specific and dynamic patterns of evolution for hearing and sound producing organs. In the suborder Ensifera, we infer that forewing-based stridulation and tibial tympanal ears co-evolved, but in the suborder Caelifera, abdominal tympanal ears first evolved in a non-sexual context, and later co-opted for sexual signalling when sound producing organs evolved. However, we find little evidence that the evolution of hearing and sound producing organs increased diversification rates in those lineages with known acoustic communication.