scholarly journals A molecular time-scale for eukaryote evolution recalibrated with the continuous microfossil record

2006 ◽  
Vol 273 (1596) ◽  
pp. 1867-1872 ◽  
Author(s):  
Cédric Berney ◽  
Jan Pawlowski
Keyword(s):  
Time Scale ◽  
Small Subunit ◽  
Molecular Dating ◽  
Time Estimates ◽  
Early Diversification ◽  
Eukaryote Evolution ◽  
Eukaryotic Origin ◽  
The Rich ◽  
Early Radiation ◽  
Relaxed Molecular Clock

Recent attempts to establish a molecular time-scale of eukaryote evolution failed to provide a congruent view on the timing of the origin and early diversification of eukaryotes. The major discrepancies in molecular time estimates are related to questions concerning the calibration of the tree. To limit these uncertainties, we used here as a source of calibration points the rich and continuous microfossil record of dinoflagellates, diatoms and coccolithophorids. We calibrated a small-subunit ribosomal RNA tree of eukaryotes with four maximum and 22 minimum time constraints. Using these multiple calibration points in a Bayesian relaxed molecular clock framework, we inferred that the early radiation of eukaryotes occurred near the Mesoproterozoic–Neoproterozoic boundary, about 1100 million years ago. Our results indicate that most Proterozoic fossils of possible eukaryotic origin cannot be confidently assigned to extant lineages and should therefore not be used as calibration points in molecular dating.

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 Undersampling Taxa Will Underestimate Molecular Divergence Dates: An Example from the South American Lizard Clade Liolaemini

2013 ◽  
Vol 2013 ◽  
pp. 1-12 ◽  
Author(s):  
James A. Schulte
Keyword(s):  
Divergence Time ◽  
Penalized Likelihood ◽  
Molecular Data ◽  
Molecular Dating ◽  
Taxon Sampling ◽  
South American ◽  
The South ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
Age Estimates

Methods for estimating divergence times from molecular data have improved dramatically over the past decade, yet there are few studies examining alternative taxon sampling effects on node age estimates. Here, I investigate the effect of undersampling species diversity on node ages of the South American lizard clade Liolaemini using several alternative subsampling strategies for both time calibrations and taxa numbers. Penalized likelihood (PL) and Bayesian molecular dating analyses were conducted on a densely sampled (202 taxa) mtDNA-based phylogenetic hypothesis of Iguanidae, including 92 Liolaemini species. Using all calibrations and penalized likelihood, clades with very low taxon sampling had node age estimates younger than clades with more complete taxon sampling. The effect of Bayesian and PL methods differed when either one or two calibrations only were used with dense taxon sampling. Bayesian node ages were always older when fewer calibrations were used, whereas PL node ages were always younger. This work reinforces two important points: (1) whenever possible, authors should strongly consider adding as many taxa as possible, including numerous outgroups, prior to node age estimation to avoid considerable node age underestimation and (2) using more, critically assessed, and accurate fossil calibrations should yield improved divergence time estimates.

scholarly journals Evaluating the Impact of Purifying Selection on Species-level Molecular Dating

2019 ◽  
Author(s):  
Chong He ◽  
Dan Liang ◽  
Peng Zhang
Keyword(s):  
Molecular Clock ◽  
Neutral Theory ◽  
Purifying Selection ◽  
Selective Constraint ◽  
Species Level ◽  
Molecular Dating ◽  
Substitution Saturation ◽  
Time Estimates ◽  
Branch Lengths ◽  
The Impact

AbstractThe neutral theory of molecular evolution suggests that the constancy of the molecular clock relies on the neutral condition. Thus, purifying selection, the most common type of natural selection, could influence the constancy of the molecular clock, and the use of genes/sites under purifying selection may produce less reliable molecular dating results. However, in current practices of species-level molecular dating, some researchers prefer to select slowly evolving genes/sites to avoid the potential impact of substitution saturation. These genes/sites are generally under a strong influence of purifying selection. Here, from the data of 23 published mammal genomes, we constructed datasets under various selective constraints. We compared the differences in branch lengths and time estimates among these datasets to investigate the impact of purifying selection on species-level molecular dating. We found that as the selective constraint increases, terminal branches are extended, which introduces biases into the result of species-level molecular dating. This result suggests that in species-level molecular dating, the impact of purifying selection should be taken into consideration, and researchers should be more cautious with the use of genes/sites under purifying selection.

scholarly journals RelTime relaxes the strict molecular clock throughout the phylogeny

2017 ◽  
Author(s):  
Fabia U. Battistuzzi ◽  
Qiqing Tao ◽  
Lance Jones ◽  
Koichiro Tamura ◽  
Sudhir Kumar
Keyword(s):  
Molecular Phylogeny ◽  
Molecular Clock ◽  
Evolutionary Rates ◽  
Molecular Dating ◽  
Divergence Times ◽  
Similar Time ◽  
Time Estimates ◽  
Theoretical Analyses ◽  
Strict Molecular Clock ◽  
Median Rate

AbstractThe RelTime method estimates divergence times when evolutionary rates vary among lineages. Theoretical analyses show that RelTime relaxes the strict molecular clock throughout a molecular phylogeny, and it performs well in the analysis of empirical and computer simulated datasets in which evolutionary rates are variable. Lozano-Fernandez et al. (2017) found that the application of RelTime to one metazoan dataset (Erwin et al. 2011) produced equal rates for several ancient lineages, which led them to speculate that RelTime imposes a strict molecular clock for deep animal divergences. RelTime does not impose a strict molecular clock. The pattern observed by Lozano-Fernandez et al. (2017) was a result of the use of an option to assign the same rate to lineages in RelTime when the rates are not statistically significantly different. The median rate difference was 5% for many deep metazoan lineages for Erwin et al. (2011) dataset, so the rate equality was not rejected. In fact, RelTime analysis with and without the option to test rate differences produced very similar time estimates. We found that the Bayesian time estimates vary widely depending on the root priors assigned, and that the use of less restrictive priors produce Bayesian divergence times that are concordant with those from RelTime for Erwin et al. (2011) dataset. Therefore, it is prudent to discuss Bayesian estimates obtained under a range of priors in any discourse about molecular dating, including method comparisons.

scholarly journals Colonization time on island settings: lessons from the Hawaiian and Canary Island floras

2019 ◽  
Vol 191 (2) ◽  
pp. 155-163 ◽  
Author(s):  
C García-Verdugo ◽  
J Caujapé-Castells ◽  
I Sanmartín
Keyword(s):  
Molecular Dating ◽  
Plant Colonization ◽  
Endemic Plant ◽  
Biogeographic Patterns ◽  
Lineage Differentiation ◽  
Time Estimates ◽  
Colonization Time ◽  
Oceanic Archipelagos ◽  
Time Of Divergence ◽  
Age Estimates

Abstract Molecular dating offers a tool for inferring the time of divergence between two lineages. In this study, we discuss how dated molecular reconstructions are informative of two different, albeit often intermingled, time estimates with regard to a fundamental process in island biogeography: the time of island colonization (TIC). We illustrate how stem age estimates provide information on the divergence between the extant island lineage and their closest relatives (i.e. the onset of lineage differentiation). Such estimates, however, are typically poor TIC predictors, as they are strongly affected by spatial and temporal uncertainty, particularly in cases of deep stem ages. Crown ages of endemic island lineages, in contrast, provide information on the temporal onset of island in situ diversification, and may represent a better proxy for TIC when the associated uncertainty is taken into account. Thus, the geographic and temporal distance separating the island and mainland lineages in phylogenetic/phylogeographic reconstructions are key factors for determining the reliability of these two estimates as proxies of TIC. We show how divergence times can be used to investigate the biogeographic patterns of two well-studied oceanic archipelagos: Hawaii and the Canary Islands. A compilation of molecular age estimates for nearly one-third of the endemic plant lineages in each archipelago reveals that Canarian plant lineages exhibit significantly younger mean crown ages (2.1 ± 2.4 Myr) than Hawaiian lineages (3.5 ± 2.9 Myr), despite island substrates being much older in the Canarian archipelago. We postulate that this pattern suggests: (1) a more important role of submerged islands during plant colonization in Hawaii, and (2) higher taxon turnover in the Canaries, mediated by relatively young (Mediterranean) lineages, and probably facilitated by the combination of the high incidence of extinction for the last 5 Myr and the close proximity of mainland source areas as compared to Hawaii.

Accounting for Uncertainty in the Evolutionary Timescale of Green Plants Through Clock-Partitioning and Fossil Calibration Strategies

2019 ◽  
Vol 69 (1) ◽  
pp. 1-16 ◽  
Author(s):  
Yuan Nie ◽  
Charles S P Foster ◽  
Tianqi Zhu ◽  
Ru Yao ◽  
David A Duchêne ◽  
...  
Keyword(s):  
Global Climate ◽  
Divergence Time ◽  
Tree Topology ◽  
Molecular Dating ◽  
Crown Group ◽  
Green Plants ◽  
Fossil Calibration ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
Chloroplast Genomes

Abstract Establishing an accurate evolutionary timescale for green plants (Viridiplantae) is essential to understanding their interaction and coevolution with the Earth’s climate and the many organisms that rely on green plants. Despite being the focus of numerous studies, the timing of the origin of green plants and the divergence of major clades within this group remain highly controversial. Here, we infer the evolutionary timescale of green plants by analyzing 81 protein-coding genes from 99 chloroplast genomes, using a core set of 21 fossil calibrations. We test the sensitivity of our divergence-time estimates to various components of Bayesian molecular dating, including the tree topology, clock models, clock-partitioning schemes, rate priors, and fossil calibrations. We find that the choice of clock model affects date estimation and that the independent-rates model provides a better fit to the data than the autocorrelated-rates model. Varying the rate prior and tree topology had little impact on age estimates, with far greater differences observed among calibration choices and clock-partitioning schemes. Our analyses yield date estimates ranging from the Paleoproterozoic to Mesoproterozoic for crown-group green plants, and from the Ediacaran to Middle Ordovician for crown-group land plants. We present divergence-time estimates of the major groups of green plants that take into account various sources of uncertainty. Our proposed timeline lays the foundation for further investigations into how green plants shaped the global climate and ecosystems, and how embryophytes became dominant in terrestrial environments.

scholarly journals The evolution of methods for establishing evolutionary timescales

2016 ◽  
Vol 371 (1699) ◽  
pp. 20160020 ◽  
Author(s):  
Philip C. J. Donoghue ◽  
Ziheng Yang
Keyword(s):  
Fossil Record ◽  
Environmental Influence ◽  
Molecular Dating ◽  
Divergence Times ◽  
Fossil Species ◽  
Time Estimates ◽  
Fossil Evidence ◽  
Probability Densities ◽  
History Of ◽  
Lineage Divergence

The fossil record is well known to be incomplete. Read literally, it provides a distorted view of the history of species divergence and extinction, because different species have different propensities to fossilize, the amount of rock fluctuates over geological timescales, as does the nature of the environments that it preserves. Even so, patterns in the fossil evidence allow us to assess the incompleteness of the fossil record. While the molecular clock can be used to extend the time estimates from fossil species to lineages not represented in the fossil record, fossils are the only source of information concerning absolute (geological) times in molecular dating analysis. We review different ways of incorporating fossil evidence in modern clock dating analyses, including node-calibrations where lineage divergence times are constrained using probability densities and tip-calibrations where fossil species at the tips of the tree are assigned dates from dated rock strata. While node-calibrations are often constructed by a crude assessment of the fossil evidence and thus involves arbitrariness, tip-calibrations may be too sensitive to the prior on divergence times or the branching process and influenced unduly affected by well-known problems of morphological character evolution, such as environmental influence on morphological phenotypes, correlation among traits, and convergent evolution in disparate species. We discuss the utility of time information from fossils in phylogeny estimation and the search for ancestors in the fossil record. This article is part of the themed issue ‘Dating species divergences using rocks and clocks’.

scholarly journals Recalibration of the insect evolutionary time scale using Monte San Giorgio fossils suggests survival of key lineages through the End-Permian Extinction

2019 ◽  
Vol 286 (1912) ◽  
pp. 20191854 ◽  
Author(s):  
Matteo Montagna ◽  
K. Jun Tong ◽  
Giulia Magoga ◽  
Laura Strada ◽  
Andrea Tintori ◽  
...  
Keyword(s):  
Time Scale ◽  
Animal Species ◽  
Soft Tissues ◽  
Internal Organs ◽  
The Face ◽  
Permian Extinction ◽  
The Rich ◽  
Extinction Events ◽  
Insect Fossils ◽  
Complete Metamorphosis

Insects are a highly diverse group of organisms and constitute more than half of all known animal species. They have evolved an extraordinary range of traits, from flight and complete metamorphosis to complex polyphenisms and advanced eusociality. Although the rich insect fossil record has helped to chart the appearance of many phenotypic innovations, data are scarce for a number of key periods. One such period is that following the End-Permian Extinction, recognized as the most catastrophic of all extinction events. We recently discovered several 240-million-year-old insect fossils in the Mount San Giorgio Lagerstätte (Switzerland–Italy) that are remarkable for their state of preservation (including internal organs and soft tissues), and because they extend the records of their respective taxa by up to 200 million years. By using these fossils as calibrations in a phylogenomic dating analysis, we present a revised time scale for insect evolution. Our date estimates for several major lineages, including the hyperdiverse crown groups of Lepidoptera, Hemiptera: Heteroptera and Diptera, are substantially older than their currently accepted post-Permian origins. We found that major evolutionary innovations, including flight and metamorphosis, appeared considerably earlier than previously thought. These results have numerous implications for understanding the evolution of insects and their resilience in the face of extreme events such as the End-Permian Extinction.

scholarly journals Taxonomy, Phylogeny, Molecular Dating and Ancestral State Reconstruction of Xylariomycetidae (Sordariomycetes)

2021 ◽  
Author(s):  
Milan C. Samarakoon ◽  
Kevin D Hyde ◽  
Sajeewa S. N. Maharachchikumbura ◽  
Marc Stadler ◽  
E. B. Gareth Jones ◽  
...  
Keyword(s):  
Divergence Time ◽  
Molecular Dating ◽  
Character State ◽  
Ancestral State ◽  
New Host ◽  
State Reconstruction ◽  
Divergence Time Estimates ◽  
New Family ◽  
Ancestral Character State ◽  
Time Estimates

Abstract Xylariomycetidae ( Ascomycota ) is a highly diversified group with variable stromatic characters. Our research focused on inconspicuous stromatic xylarialean taxa from China, Italy, Russia, Thailand and the United Kingdom. Detailed morphological descriptions, illustrations and combined ITS-LSU- rpb 2- tub 2- tef 1 phylogenies revealed 38 taxa from our collections belonging to Amphisphaeriales and Xylariales . A new family ( Appendicosporaceae ), five new genera ( Magnostiolata , Melanostictus , Neoamphisphaeria , Nigropunctata and Paravamsapriya ), 27 new species ( Acrocordiella photiniicola , Allocryptovalsa sichuanensis , Amphisphaeria parvispora , Anthostomella lamiacearum , Apiospora guiyangensis , Ap. sichuanensis , Biscogniauxia magna , Eutypa camelliae , Helicogermslita clypeata , Hypocopra zeae , Magnostiolata mucida , Melanostictus longiostiolatus , Me. thailandicus , Nemania longipedicellata , Ne. delonicis , Ne. paraphysata , Ne. thailandensis , Neoamphisphaeria hyalinospora , Neoanthostomella bambusicola , Nigropunctata bambusicola , Ni. nigrocircularis , Ni. thailandica , Occultitheca rosae , Paravamsapriya ostiolata , Peroneutypa leucaenae , Seiridium italicum and Vamsapriya mucosa ) and seven new host/geographical records are introduced and reported. Divergence time estimates indicate that Delonicicolales diverged from Amphisphaeriales + Xylariales at 161 (123–197) MYA. Amphisphaeriales and Xylariales diverged 154 (117–190) MYA with a crown age of 127 (92–165) MYA and 147 (111–184) MYA, respectively. Appendicosporaceae ( Amphisphaeriales ) has a stem age of 89 (65–117) MYA. Ancestral character state reconstruction indicates that astromatic, clypeate ascomata with aseptate, hyaline ascospores that lack germ slits may probably be ancestral Xylariomycetidae having plant-fungal endophytic associations. The Amphisphaeriales remained mostly astromatic with common septate, hyaline ascospores. Stromatic variations may have developed mostly during the Cretaceous period. Brown ascospores are common in Xylariales , but they first appeared in Amphisphaeriaceae , Melogrammataceae and Sporocadaceae during the early Cretaceous. The ascospore germ slits appeared only in Xylariales during the Cretaceous after the divergence of Lopadostomataceae . Hyaline, filiform and apiospores may have appeared as separate lineages providing the basis to Xylariaceae , which may have diverged independently. The future classification of polyphyletic xylarialean taxa will not be based on stromatic variations, but the type of ring, the colour of the ascospores, and the presence or absence of the type of germ slit.

scholarly journals Phylogenomic relationships and historical biogeography in the South American vegetable ivory palms (Phytelepheae)

2020 ◽  
Author(s):  
Sebastián Escobar ◽  
Andrew J. Helmstetter ◽  
Rommel Montúfar ◽  
Thomas L. P. Couvreur ◽  
Henrik Balslev
Keyword(s):  
Phylogenetic Relationships ◽  
Divergence Time ◽  
Historical Biogeography ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
Early Diversification ◽  
Time Calibration ◽  
Vegetable Ivory ◽  
Andean Uplift ◽  
Magdalena River

AbstractThe vegetable ivory palms (Phytelepheae) form a small group of Neotropical palms whose phylogenetic relationships are not fully understood. Three genera and eight species are currently recognized; however, it has been suggested that Phytelephas macrocarpa could include the species Phytelephas seemannii and Phytelephas schottii because of supposed phylogenetic relatedness and similar morphology. We inferred their phylogenetic relationships and divergence time estimates using the 32 most clock-like loci of a custom palm bait-kit formed by 176 genes and four fossils for time calibration. We additionally explored the historical biogeography of the tribe under the recovered phylogenetic relationships. Our fossil-dated tree showed the eight species previously recognized, and that P. macrocarpa is not closely related to P. seemanii and P. schottii, which, as a consequence, should not be included in P. macrocarpa. The ancestor of the vegetable ivory palms was widely-distributed in the Chocó, the inter-Andean valley of the Magdalena River, and the Amazonia during the Miocene at 19.25 Ma. Early diversification in Phytelephas at 5.27 Ma can be attributed to trans-Andean vicariance between the Chocó/Magdalena and the Amazonia. Our results support the role of Andean uplift in the early diversification of Phytelephas under new phylogenetic relationships inferred from genomic data.

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