scholarly journals What drives results in Bayesian morphological clock analyses?

2017 ◽  
Author(s):  
Caroline Parins-Fukuchi ◽  
Joseph W. Brown
Keyword(s):  
Morphological Evolution ◽  
Divergence Time ◽  
Morphological Characters ◽  
Morphological Data ◽  
Divergence Times ◽  
High Profile ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
Geological Information ◽  
Positive Effect

AbstractRecently, approaches that estimate species divergence times using fossil taxa and models of morphological evolution have exploded in popularity. These methods incorporate diverse biological and geological information to inform posterior reconstructions, and have been applied to several high-profile clades to positive effect. However, there are important examples where morphological data are misleading, resulting in unrealistic age estimates. While several studies have demonstrated that these approaches can be robust and internally consistent, the causes and limitations of these patterns remain unclear. In this study, we dissect signal in Bayesian dating analyses of three mammalian clades. For two of the three examples, we find that morphological characters provide little information regarding divergence times as compared to geological range information, with posterior estimates largely recapitulating those recovered under the prior. However, in the cetacean dataset, we find that morphological data do appreciably inform posterior divergence time estimates. We supplement these empirical analyses with a set of simulations designed to explore the efficiency and limitations of binary and 3-state character data in reconstructing node ages. Our results demonstrate areas of both strength and weakness for morphological clock analyses, and help to outline conditions under which they perform best and, conversely, when they should be eschewed in favour of purely geological approaches.

scholarly journals Molecular and morphological clocks for estimating evolutionary divergence times

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Jose Barba-Montoya ◽  
Qiqing Tao ◽  
Sudhir Kumar
Keyword(s):  
Divergence Time ◽  
Morphological Characters ◽  
Molecular Data ◽  
Morphological Data ◽  
Divergence Times ◽  
Evolutionary Divergence ◽  
Species Divergence ◽  
Time Estimates ◽  
Branch Lengths ◽  
Morphological And Molecular Data

Abstract Background Matrices of morphological characters are frequently used for dating species divergence times in systematics. In some studies, morphological and molecular character data from living taxa are combined, whereas others use morphological characters from extinct taxa as well. We investigated whether morphological data produce time estimates that are concordant with molecular data. If true, it will justify the use of morphological characters alongside molecular data in divergence time inference. Results We systematically analyzed three empirical datasets from different species groups to test the concordance of species divergence dates inferred using molecular and discrete morphological data from extant taxa as test cases. We found a high correlation between their divergence time estimates, despite a poor linear relationship between branch lengths for morphological and molecular data mapped onto the same phylogeny. This was because node-to-tip distances showed a much higher correlation than branch lengths due to an averaging effect over multiple branches. We found that nodes with a large number of taxa often benefit from such averaging. However, considerable discordance between time estimates from molecules and morphology may still occur as  some intermediate nodes may show large time differences between these two types of data. Conclusions Our findings suggest that node- and tip-calibration approaches may be better suited for nodes with many taxa. Nevertheless, we highlight the importance of evaluating the concordance of intrinsic time structure in morphological and molecular data before any dating analysis using combined datasets.

scholarly journals Molecular and morphological clocks for estimating evolutionary divergence times

2021 ◽  
Author(s):  
Jose Barba-Montoya ◽  
Qiqing Tao ◽  
Sudhir Kumar
Keyword(s):  
Divergence Time ◽  
Morphological Characters ◽  
Molecular Data ◽  
Morphological Data ◽  
Divergence Times ◽  
Evolutionary Divergence ◽  
Species Divergence ◽  
Time Estimates ◽  
Branch Lengths ◽  
Morphological And Molecular Data

Abstract Background: Matrices of morphological characters are frequently used for dating species divergence times in systematics. In some studies, morphological and molecular character data from living taxa are combined, whereas others use morphological characters from extinct taxa as well. We investigated whether morphological data produce time estimates that are concordant with molecular data. If true, it will justify the use of morphological characters alongside molecular data in divergence time inference.Results: We systematically analyzed three empirical datasets from different species groups to test the concordance of species divergence dates inferred using molecular and discrete morphological data from extant taxa as test cases. We found a high correlation between their divergence time estimates, despite a poor linear relationship between branch lengths for morphological and molecular data mapped onto the same phylogeny. This was because node-to-tip distances showed a much higher correlation than branch lengths due to an averaging effect over multiple branches. We found that nodes with a large number of taxa often benefit from such averaging. However, considerable discordance between time estimates from molecules and morphology may still occur because some deeper nodes show a large time differences between these two types of data.Conclusions: Our findings suggest that node- and tip-calibration approaches may be better suited for nodes with many taxa. Nevertheless, we highlight the importance of evaluating the concordance of time structure in morphological and molecular data before any dating analysis using combined datasets.

scholarly journals Molecular and morphological clocks for estimating evolutionary divergence times

2021 ◽  
Author(s):  
Jose Barba-Montoya ◽  
Qiqing Tao ◽  
Sudhir Kumar
Keyword(s):  
Divergence Time ◽  
Morphological Characters ◽  
Molecular Data ◽  
Morphological Data ◽  
Divergence Times ◽  
Evolutionary Divergence ◽  
Species Divergence ◽  
Time Estimates ◽  
Branch Lengths ◽  
Morphological And Molecular Data

Abstract Background: Matrices of morphological characters are frequently used for dating species divergence times in systematics. In some studies, morphological and molecular character data from living taxa are combined, whereas others use morphological characters from extinct taxa as well. We investigated whether morphological data produce time estimates that are concordant with molecular data. If true, it will justify the use of morphological characters alongside molecular data in divergence time inference.Results: We systematically analyzed three empirical datasets from different species groups to test the concordance of species divergence dates inferred using molecular and discrete morphological data from extant taxa as test cases. We found a high correlation between their divergence time estimates, despite a poor linear relationship between branch lengths for morphological and molecular data mapped onto the same phylogeny. This was because node-to-tip distances showed a much higher correlation than branch lengths due to an averaging effect over multiple branches. We found that nodes with a large number of taxa often benefit from such averaging. However, considerable discordance between time estimates from molecules and morphology may still occur because some deeper nodes may show large time differences between these two types of data.Conclusions: Our findings suggest that node- and tip-calibration approaches may be better suited for nodes with many taxa. Nevertheless, we highlight the importance of evaluating the concordance of intrinsic time structure in morphological and molecular data before any dating analysis using combined datasets.

scholarly journals Molecular and morphological clocks for estimating evolutionary divergence times

2020 ◽  
Author(s):  
Jose Barba-Montoya ◽  
Qiqing Tao ◽  
Sudhir Kumar
Keyword(s):  
Divergence Time ◽  
Morphological Characters ◽  
Molecular Data ◽  
Morphological Data ◽  
Divergence Times ◽  
Evolutionary Divergence ◽  
Species Divergence ◽  
Time Estimates ◽  
Branch Lengths ◽  
Morphological And Molecular Data

Abstract Background: Matrices of morphological characters are frequently used for dating species divergence times in systematics. In some studies, morphological and molecular character data from living taxa are combined, whereas others use morphological characters from extinct taxa as well. We investigated whether morphological data produce time estimates that are concordant with molecular data. If true, it will justify the use of morphological characters alongside molecular data in divergence time inference. Results: We systematically analyzed three empirical datasets from different species groups to test the concordance of dates of species divergence inferred using molecular and discrete morphological data from extant taxa as test cases. We found a high correlation between their divergence time estimates, despite a poor linear relationship between branch lengths for morphological and molecular data mapped onto the same phylogeny. This was because node-to-tip distances showed a much higher correlation than branch lengths, because of an averaging effect over multiple branches. We found that nodes with a large number of taxa often benefit from such averaging, but some considerable discordance between time estimates from molecules and morphology may still occur because some deeper branches show large difference from two types of data. Conclusions: Our findings suggest that node- and tip-calibration approaches may be better suited for nodes with a large number of taxa. Nevertheless, we highlight the importance of evaluating the concordance of time structure in morphological and molecular data before any dating analysis using combined datasets.

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.

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

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.

scholarly journals Notes, outline and divergence times of Basidiomycota

2019 ◽  
Vol 99 (1) ◽  
pp. 105-367 ◽  
Author(s):  
Mao-Qiang He ◽  
Rui-Lin Zhao ◽  
Kevin D. Hyde ◽  
Dominik Begerow ◽  
Martin Kemler ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Divergence Time ◽  
Divergence Times ◽  
Sequence Information ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
The Family ◽  
Life Mode ◽  
Species Type ◽  
Phylogeny And Evolution

AbstractThe Basidiomycota constitutes a major phylum of the kingdom Fungi and is second in species numbers to the Ascomycota. The present work provides an overview of all validly published, currently used basidiomycete genera to date in a single document. An outline of all genera of Basidiomycota is provided, which includes 1928 currently used genera names, with 1263 synonyms, which are distributed in 241 families, 68 orders, 18 classes and four subphyla. We provide brief notes for each accepted genus including information on classification, number of accepted species, type species, life mode, habitat, distribution, and sequence information. Furthermore, three phylogenetic analyses with combined LSU, SSU, 5.8s, rpb1, rpb2, and ef1 datasets for the subphyla Agaricomycotina, Pucciniomycotina and Ustilaginomycotina are conducted, respectively. Divergence time estimates are provided to the family level with 632 species from 62 orders, 168 families and 605 genera. Our study indicates that the divergence times of the subphyla in Basidiomycota are 406–430 Mya, classes are 211–383 Mya, and orders are 99–323 Mya, which are largely consistent with previous studies. In this study, all phylogenetically supported families were dated, with the families of Agaricomycotina diverging from 27–178 Mya, Pucciniomycotina from 85–222 Mya, and Ustilaginomycotina from 79–177 Mya. Divergence times as additional criterion in ranking provide additional evidence to resolve taxonomic problems in the Basidiomycota taxonomic system, and also provide a better understanding of their phylogeny and evolution.

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

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 ◽  
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.

scholarly journals Relative efficiencies of simple and complex substitution models in estimating divergence times in phylogenomics

2020 ◽  
Author(s):  
Qiqing Tao ◽  
Jose Barba-Montoya ◽  
Louise A. Huuki ◽  
Mary Kathleen Durnan ◽  
Sudhir Kumar
Keyword(s):  
Divergence Time ◽  
Sequence Divergence ◽  
Model Complexity ◽  
Divergence Times ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
Complex Models ◽  
The Difference ◽  
Diverse Groups ◽  
Simple Models

AbstractThe conventional wisdom in molecular evolution is to apply parameter-rich models of nucleotide and amino acid substitutions for estimating divergence times. However, the actual extent of the difference between time estimates produced by highly complex models compared to those from simple models is yet to be quantified for contemporary datasets that frequently contain sequences from many species and genes. In a reanalysis of many large multispecies alignments from diverse groups of taxa using the same tree topologies and calibrations, we found that the use of the simplest models can produce divergence time estimates and credibility intervals similar to those obtained from the complex models applied in the original studies. This result is surprising because the use of simple models underestimates sequence divergence for all the datasets analyzed. We find three fundamental reasons for the observed robustness of time estimates to model complexity in many practical datasets. First, the estimates of branch lengths and node-to-tip distances under the simplest model show an approximately linear relationship with those produced by using the most complex models applied, especially for datasets with many sequences. Second, relaxed clock methods automatically adjust rates on branches that experience considerable underestimation of sequence divergences, resulting in time estimates that are similar to those from complex models. And, third, the inclusion of even a few good calibrations in an analysis can reduce the difference in time estimates from simple and complex models. The robustness of time estimates to models complexity in these empirical data analyses is encouraging, because all phylogenomics studies use statistical models that are oversimplified descriptions of actual evolutionary substitution processes.

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

2020 ◽  
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

AbstractMotivationAs 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.ResultsWe 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.AvailabilityAll datasets are deposited in Figshare: https://doi.org/10.6084/[email protected]

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