scholarly journals Timing the extant avian radiation: The rise of modern birds, and the importance of modeling molecular rate variation

2019 ◽  
Author(s):  
Daniel J. Field ◽  
Jacob S. Berv ◽  
Allison Y. Hsiang ◽  
Robert Lanfear ◽  
Michael J. Landis ◽  
...  
Keyword(s):  
Mass Extinction ◽  
Fossil Record ◽  
Alternative Hypothesis ◽  
Model Misspecification ◽  
Divergence Time ◽  
Rate Variation ◽  
Substitution Rates ◽  
Multiple Paths ◽  
The Impact ◽  
Rates Of Molecular Evolution

Unravelling the phylogenetic relationships among the major groups of living birds has been described as the greatest outstanding problem in dinosaur systematics. Recent work has identified portions of the avian tree of life that are particularly challenging to reconstruct, perhaps as a result of rapid cladogenesis early in crown bird evolutionary history (specifically, the interval immediately following the end-Cretaceous mass extinction). At face value this hypothesis enjoys support from the crown bird fossil record, which documents the first appearances of most major crown bird lineages in the early Cenozoic—in line with a model of rapid post-extinction niche filling among surviving avian lineages. However, molecular-clock analyses have yielded strikingly variable estimates for the age of crown birds, and conflicting inferences on the impact of the end-Cretaceous mass extinction on the extant bird radiation. This uncertainty has often been ascribed to a patchy avian fossil record, but the possibility of model misspecification in molecular divergence time analyses represents an important and relatively underexplored alternative hypothesis. Here, we highlight the necessity of further developing and using models that account for coordinated variation in rates of molecular evolution across a phylogeny (e.g. molecular early bursts) as a means of assessing support for a rapid post-Cretaceous radiation of crown birds. We discuss how relationships between life-history and substitution rates can mislead divergence time studies that do not account for directional changes in substitution rates over time, and suggest that these effects might have caused some of the variation in existing molecular date estimates for birds. We suggest multiple paths forward that could help resolve this and similar conflicts within other major eukaryotic clades.

scholarly journals Timing the extant avian radiation: The rise of modern birds, and the importance of modeling molecular rate variation

2019 ◽  
Author(s):  
Daniel J. Field ◽  
Jacob S. Berv ◽  
Allison Y. Hsiang ◽  
Robert Lanfear ◽  
Michael J. Landis ◽  
...  
Keyword(s):  
Mass Extinction ◽  
Fossil Record ◽  
Alternative Hypothesis ◽  
Model Misspecification ◽  
Divergence Time ◽  
Rate Variation ◽  
Substitution Rates ◽  
Multiple Paths ◽  
The Impact ◽  
Rates Of Molecular Evolution

Unravelling the phylogenetic relationships among the major groups of living birds has been described as the greatest outstanding problem in dinosaur systematics. Recent work has identified portions of the avian tree of life that are particularly challenging to reconstruct, perhaps as a result of rapid cladogenesis early in crown bird evolutionary history (specifically, the interval immediately following the end-Cretaceous mass extinction). At face value this hypothesis enjoys support from the crown bird fossil record, which documents the first appearances of most major crown bird lineages in the early Cenozoic—in line with a model of rapid post-extinction niche filling among surviving avian lineages. However, molecular-clock analyses have yielded strikingly variable estimates for the age of crown birds, and conflicting inferences on the impact of the end-Cretaceous mass extinction on the extant bird radiation. This uncertainty has often been ascribed to a patchy avian fossil record, but the possibility of model misspecification in molecular divergence time analyses represents an important and relatively underexplored alternative hypothesis. Here, we highlight the necessity of further developing and using models that account for coordinated variation in rates of molecular evolution across a phylogeny (e.g. molecular early bursts) as a means of assessing support for a rapid post-Cretaceous radiation of crown birds. We discuss how relationships between life-history and substitution rates can mislead divergence time studies that do not account for directional changes in substitution rates over time, and suggest that these effects might have caused some of the variation in existing molecular date estimates for birds. We suggest multiple paths forward that could help resolve this and similar conflicts within other major eukaryotic clades.

scholarly journals Investigating the reliability of molecular estimates of evolutionary time when substitution rates and speciation rates vary

2021 ◽  
Author(s):  
Andrew M Ritchie ◽  
Xia Hua ◽  
Lindell Bromham
Keyword(s):  
Dna Sequences ◽  
Empirical Studies ◽  
Divergence Time ◽  
Molecular Dating ◽  
Rate Variation ◽  
Substitution Rates ◽  
Molecular Change ◽  
Dna Evidence ◽  
Dating Methods ◽  
Speciation Rates

Background An accurate timescale of evolutionary history is essential to testing hypotheses about the influence of historical events and processes, and the timescale for evolution is increasingly derived from analysis of DNA sequences. But variation in the rate of molecular evolution complicates the inference of time from DNA. Evidence is growing for numerous factors, such as life history and habitat, that are linked both to the molecular processes of mutation and fixation and to rates of macroevolutionary diversification. However, the most widely used models of molecular rate variation, such as the uncorrelated and autocorrelated lognormal clocks, rely on idealised models of rate variation and molecular dating methods are rarely tested against complex models of rate change. One relationship that is not accounted for in molecular dating is the potential for interaction between molecular substitution rates and speciation, a relationship that has been supported by empirical studies in a growing number of taxa. If these relationships are as widespread as evidence indicates, they may have a significant influence on molecular dates. Results We simulate phylogenies and molecular sequences under three different realistic rate variation models - one in which speciation rates and substitution rates both vary but are unlinked, one in which they covary continuously and one punctuated model in which molecular change is concentrated in speciation events, using empirical case studies to parameterise realistic simulations. We test two commonly used "relaxed clock" molecular dating methods against these realistic simulations to explore the degree of error in molecular dates under each model. We find average divergence time inference errors ranging from 12% of node age for the unlinked model when reconstructed under an uncorrelated rate prior, to up to 93% when punctuated simulations are reconstructed under an autocorrelated prior. Conclusions We demonstrate the potential for substantial errors in molecular dates when both speciation rates and substitution rates vary between lineages. This study highlights the need for tests of molecular dating methods against realistic models of rate variation generated from empirical parameters and known relationships.

scholarly journals The Implications of Lineage-Specific Rates for Divergence Time Estimation

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 ◽  
Divergence Time Estimation ◽  
Divergence Time Estimates ◽  
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.]

scholarly journals A Hiatus Obscures the Early Evolution of Modern Lineages of Bony Fishes

2021 ◽  
Vol 8 ◽  
Author(s):  
Carlo Romano
Keyword(s):  
Mass Extinction ◽  
Fossil Record ◽  
Middle Triassic ◽  
Early Evolution ◽  
Early Triassic ◽  
Triassic Boundary ◽  
Bony Fishes ◽  
Extinction Event ◽  
Mass Extinction Event ◽  
The Impact

About half of all vertebrate species today are ray-finned fishes (Actinopterygii), and nearly all of them belong to the Neopterygii (modern ray-fins). The oldest unequivocal neopterygian fossils are known from the Early Triassic. They appear during a time when global fish faunas consisted of mostly cosmopolitan taxa, and contemporary bony fishes belonged mainly to non-neopterygian (“paleopterygian”) lineages. In the Middle Triassic (Pelsonian substage and later), less than 10 myrs (million years) after the Permian-Triassic boundary mass extinction event (PTBME), neopterygians were already species-rich and trophically diverse, and bony fish faunas were more regionally differentiated compared to the Early Triassic. Still little is known about the early evolution of neopterygians leading up to this first diversity peak. A major factor limiting our understanding of this “Triassic revolution” is an interval marked by a very poor fossil record, overlapping with the Spathian (late Olenekian, Early Triassic), Aegean (Early Anisian, Middle Triassic), and Bithynian (early Middle Anisian) substages. Here, I review the fossil record of Early and Middle Triassic marine bony fishes (Actinistia and Actinopterygii) at the substage-level in order to evaluate the impact of this hiatus–named herein the Spathian–Bithynian gap (SBG)–on our understanding of their diversification after the largest mass extinction event of the past. I propose three hypotheses: 1) the SSBE hypothesis, suggesting that most of the Middle Triassic diversity appeared in the aftermath of the Smithian-Spathian boundary extinction (SSBE; ∼2 myrs after the PTBME), 2) the Pelsonian explosion hypothesis, which states that most of the Middle Triassic ichthyodiversity is the result of a radiation event in the Pelsonian, and 3) the gradual replacement hypothesis, i.e. that the faunal turnover during the SBG was steady and bony fishes were not affected by extinction events subsequent to the PTBME. Based on current knowledge, hypothesis three is favored herein, but further studies are necessary to test alternative hypotheses. In light of the SBG, claims of a protracted diversification of bony fishes after the PTBME should be treated with caution.

Gastropod phylogenetics: Progress, problems, and implications

2001 ◽  
Vol 75 (6) ◽  
pp. 1128-1140 ◽  
Author(s):  
Peter J. Wagner
Keyword(s):  
Monte Carlo ◽  
Molecular Evolution ◽  
Mass Extinction ◽  
Fossil Record ◽  
Null Hypothesis ◽  
Model Group ◽  
Rates Of Evolution ◽  
Order Of Magnitude ◽  
Morphologic Evolution ◽  
Rates Of Molecular Evolution

Twentieth century fossil gastropod systematics relied extensively on neontological paradigms. However, recent appreciation of the extant gastropod diversity suggests that those early paradigms provided very unsound models. This likely is a greater problem for Paleozoic taxa than for Meso-Cenozoic gastropods because Meso-Cenozoic taxa frequently have easily recognized extant relatives whereas Paleozoic taxa frequently do not. Also, many of the taxa that apparently diverged in the Paleozoic now are limpets and retain little information about the morphologies of their coiled ancestors.Snails could be a model taxon for investigating macroevolutionary patterns because of the clade's dense fossil record. However, paleontologists usually study only adult shells (teleoconchs), and many malacologists maintain that teleoconch characters reflect phytogeny poorly if at all. This is important because many macroevolutionary hypotheses make their most specific predictions given phylogeny. Studies evaluating species- or genus-level relationships typically use more shell characters and states than do studies evaluating suprageneric relationships, as expected if shells evolve rapidly. Monte Carlo tests reject a null hypothesis that rates of homoplasy are equal among shell and soft-anatomy characters for two neogastropod clades, but suggest that these rates differ by less than an order of magnitude. Finally, teleoconch characters fail to unite bellerophontiform species with gastropod muscle scars but successfully unites clusters bellerophontiform species with tergomyan muscle scars. These results corroborate the conventional wisdom that teleoconch character distributions reflect abundant homoplasy, but the results also suggest that these distributions reflect phylogeny, too.If we can control the effects of homoplasy, then gastropods are an excellent “model” group for testing macroevolutionary hypotheses such as changing rates of evolution. Two obvious candidates are rates of morphologic evolution among basal neogastropods, and rates of molecular evolution within clades radiating after the K/T mass extinction.

scholarly journals Illustrating phylogenetic placement of fossils using RoguePlots: An example from ichneumonid parasitoid wasps (Hymenoptera, Ichneumonidae) and an extensive morphological matrix

2018 ◽  
Author(s):  
Seraina Klopfstein ◽  
Tamara Spasojevic
Keyword(s):  
Fossil Record ◽  
Morphological Evolution ◽  
Phylogenetic Analyses ◽  
Model Misspecification ◽  
Primary Source ◽  
Parasitoid Wasps ◽  
Rate Variation ◽  
Marginal Likelihoods ◽  
History Of ◽  
The Individual

AbstractThe fossil record constitutes the primary source of information about the evolutionary history of extant and extinct groups, and many analyses of macroevolution rely on fossils that are accurately placed within phylogenies. To avoid misinterpretation of the fossil record, especially by non-palaeontologists, the proper assessment and communication of uncertainty in fossil placement is crucial. We here use Bayesian morphological phylogenetics to evaluate the classifications of fossil parasitoid wasps (Hymenoptera, Ichneumonidae) and introduce ‘RoguePlots’ to illustrate placement uncertainty on the phylogeny of extant taxa. Based on an extensive, newly constructed morphological matrix of 222 characters in 24 fossil and 103 extant taxa, we test three different aspects of models of morphological evolution. We find that a model that includes ordered characters, among-character rate variation, and a state-space restricted to observed states achieves the highest marginal likelihoods. The individual RoguePlots reveal large differences in confidence in the placement of the different fossils and allow some refinements to their classification: Polyhelictes bipolarus and Ichninsum appendicrassum are moved from an uncertain subfamily placement to Pimplinae, Plectiscidea lanhami is transferred to Allomacrus in Cylloceriinae (Allomacrus lanhami, comb. nov.), Lithotorus cressoni is moved from Diplazontinae to Orthocentrinae, and we note uncertainty in the generic placement of Xanthopimpla? messelensis. We discuss potential artefacts that might result in biased posterior probabilities in Bayesian morphological phylogenetic analyses, pertaining to character and taxon sampling, fossilization biases, and model misspecification. Finally, we suggest future directions both in ichneumonid palaeontology, in the modelling of morphological evolution, and in the way Bayesian phylogenetics can improve both assessment and representation of fossil placement uncertainty.

scholarly journals Insights from Empirical Analyses and Simulations on Using Multiple Fossil Calibrations with Relaxed Clocks to Estimate Divergence Times

2020 ◽  
Vol 37 (5) ◽  
pp. 1508-1529
Author(s):  
Tom Carruthers ◽  
Robert W Scotland
Keyword(s):  
Fossil Record ◽  
Sequence Data ◽  
Divergence Time ◽  
Time Estimation ◽  
Death Process ◽  
Divergence Times ◽  
Rate Variation ◽  
Direct Information ◽  
Divergence Time Estimates ◽  
Calibration Methods

Abstract Relaxed clock methods account for among-branch-rate-variation when estimating divergence times by inferring different rates for individual branches. In order to infer different rates for individual branches, important assumptions are required. This is because molecular sequence data do not provide direct information about rates but instead provide direct information about the total number of substitutions along any branch, which is a product of the rate and time for that branch. Often, the assumptions required for estimating rates for individual branches depend heavily on the implementation of multiple fossil calibrations in a single phylogeny. Here, we show that the basis of these assumptions is often critically undermined. First, we highlight that the temporal distribution of the fossil record often violates key assumptions of methods that use multiple fossil calibrations with relaxed clocks. With respect to “node calibration” methods, this conclusion is based on our inference that different fossil calibrations are unlikely to reflect the relative ages of different clades. With respect to the fossilized birth–death process, this conclusion is based on our inference that the fossil recovery rate is often highly heterogeneous. We then demonstrate that methods of divergence time estimation that use multiple fossil calibrations are highly sensitive to assumptions about the fossil record and among-branch-rate-variation. Given the problems associated with these assumptions, our results highlight that using multiple fossil calibrations with relaxed clocks often does little to improve the accuracy of divergence time estimates.

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

2017 ◽  
Author(s):  
Joseph W. Brown ◽  
Stephen A. Smith
Keyword(s):  
Bayesian Analysis ◽  
Early Cretaceous ◽  
Fossil Record ◽  
Divergence Time ◽  
Time Estimation ◽  
Inference Problem ◽  
Divergence Time Estimation ◽  
Divergence Time Estimates ◽  
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 ◽  
2009 ◽  
Vol 2107 (1) ◽  
pp. 41-52 ◽  
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.

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

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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