scholarly journals Using Fossils to Break Long Branches in Molecular Dating: A Comparison of Relaxed Clocks Applied to the Origin of Angiosperms

2010 ◽  
Vol 59 (4) ◽  
pp. 384-399 ◽  
Author(s):  
Susana Magallón
Keyword(s):  
Molecular Dating ◽  
Origin Of Angiosperms

Pseudogenized Amelogenin Reveals Early Tooth Loss in True Toads (Anura: Bufonidae)

2021 ◽  
Author(s):  
John Shaheen ◽  
Austin B Mudd ◽  
Thomas G H Diekwisch ◽  
John Abramyan
Keyword(s):  
Tooth Loss ◽  
Tooth Enamel ◽  
Synonymous Substitution ◽  
Bufo Bufo ◽  
Molecular Dating ◽  
Bufo Gargarizans ◽  
The Family ◽  
Synonymous Substitution Rates ◽  
Mandibular Teeth ◽  
Early Tooth Loss

Abstract Extant anurans (frogs and toads) exhibit reduced dentition, ranging from a lack of mandibular teeth to complete edentulation, as observed in the true toads of the family Bufonidae. The evolutionary timeline of these reductions remains vague due to a poor fossil record. Previous studies have demonstrated an association between the lack of teeth in edentulous vertebrates and the pseudogenization of the major tooth enamel gene amelogenin (AMEL) through accumulation of deleterious mutations and the disruption of its coding sequence. In the present study we have harnessed the pseudogenization of AMEL as a molecular dating tool to correlate loss of dentition with genomic mutation patterns during the rise of the family Bufonidae. Specifically, we have utilized AMEL pseudogenes in three members of the family as a tool to estimate the putative date of edentulation in true toads. Comparison of AMEL sequences from Rhinella marina, Bufo gargarizans and Bufo bufo, with nine extant, dentulous frogs, revealed mutations confirming AMEL inactivation in Bufonidae. AMEL pseudogenes in modern bufonids also exhibited remarkably high 86–93% sequence identity among each other, with only a slight increase in substitution rate and relaxation of selective pressure, in comparison to functional copies in other anurans. Moreover, using selection intensity estimates and synonymous substitution rates, analysis of functional and pseudogenized AMEL resulted in an estimated inactivation window of 46-60 MYA in the lineage leading to modern true toads, a timeline that coincides with the rise of the family Bufonidae.

scholarly journals Climate variability impacts on diversification processes in a biodiversity hotspot: a phylogeography of ancient pseudoscorpions in south-western Australia

2019 ◽  
Vol 186 (4) ◽  
pp. 934-949 ◽  
Author(s):  
Danilo Harms ◽  
J Dale Roberts ◽  
Mark S Harvey
Keyword(s):  
Phylogenetic Analyses ◽  
Distribution Patterns ◽  
Biodiversity Hotspot ◽  
Molecular Dating ◽  
Environmental Niche ◽  
Ecological Niche Models ◽  
The South ◽  
Niche Modelling ◽  
South West ◽  
Western Division

Abstract The south-western division of Australia is the only biodiversity hotspot in Australia and is well-known for extreme levels of local endemism. Climate change has been identified as a key threat for flora and fauna, but very few data are presently available to evaluate its impact on invertebrate fauna. Here, we derive a molecular phylogeography for pseudoscorpions of the genus Pseudotyrannochthonius that in the south-west are restricted to regions with the highest rainfall. A dated molecular phylogeny derived from six gene fragments is used for biogeographic reconstruction analyses, spatial mapping, environmental niche-modelling, and to infer putative species. Phylogenetic analyses uncover nine clades with mostly allopatric distributions and often small linear ranges between 0.5 and 130 km. Molecular dating suggests that the origins of contemporary diversity fall into a period of warm/humid Palaeogene climates, but splits in the phylogeny coincide with major environmental shifts, such as significant global cooling during the Middle Miocene. By testing several models of historical biogeography available for the south-west, we determine that Pseudotyrannochthonius is an ancient relict lineage that principally follows a model of allopatric speciation in mesic zone refugia, although there are derivations from this model in that some species are older and distribution patterns more complex than expected. Ecological niche models indicate that drier and warmer future climates will lead to range contraction towards refugia of highest rainfall, probably mimicking past variations that have generated high diversity in these areas. Their conservation management will be crucial for preserving the unique biodiversity heritage of the south-west.

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.

The Currently Earliest Angiosperm Fruit from the Jurassic of North America

2021 ◽  
Vol 2 (4) ◽  
Author(s):  
Xin Wang
Keyword(s):  
North America ◽  
Early Cretaceous ◽  
Middle Jurassic ◽  
Early Evolution ◽  
The North ◽  
Plant Group ◽  
Ecological Radiation ◽  
Origin Of Angiosperms ◽  
Crucial Test

Angiosperms are the single most important plant group in the current ecosystem. However, little is known about the origin and early evolution of angiosperms. Jurassic and earlier traces of angiosperms have been claimed multiple times from Europe and Asia, but reluctance to accept these records remains. To test the truthfulness of these claims, palaeobotanical records from continents other than Europe and Asia constitute a crucial test. Here I document a new angiosperm fruit, Dilcherifructus mexicana gen. et sp. nov, from the Middle Jurassic of Mexico. Its Jurassic age suggests that origin of angiosperms is much earlier than widely accepted, while its occurrence in the North America indicates that angiosperms were already widespread in the Jurassic, although they were still far away from their ecological radiation, which started in the Early Cretaceous.

Impact of the choices of calibration points for molecular dating: a case study of Ensifera

2021 ◽  
Vol 4 (3) ◽  
Author(s):  
ANDRÉ NEL
Keyword(s):  
Molecular Dating ◽  
Rigorous Approach ◽  
Phylogenetic Studies

Fossils are crucial for molecular clade dating (Warnock et al., 2012, 2015). But it is necessary to have a rigorous approach, without rejecting taxa on poor arguments or ignoring some of them without any reasons. Here we show through two very recent examples of phylogenetic studies on the Orthoptera, that such behaviours can have dramatic consequences on the value of the results of the studies.

scholarly journals Molecular dating of phylogenetic divergence between Urochloa species based on complete chloroplast genomes

BMC Genomics ◽  
2017 ◽  
Vol 18 (1) ◽  
Author(s):  
Marco Pessoa-Filho ◽  
Alexandre Magalhães Martins ◽  
Márcio Elias Ferreira
Keyword(s):  
Molecular Dating ◽  
Chloroplast Genomes ◽  
Phylogenetic Divergence

scholarly journals Flying rocks and flying clocks: disparity in fossil and molecular dates for birds

2014 ◽  
Vol 281 (1788) ◽  
pp. 20140677 ◽  
Author(s):  
Daniel T. Ksepka ◽  
Jessica L. Ware ◽  
Kristin S. Lamm
Keyword(s):  
Analytical Methods ◽  
Fossil Record ◽  
Tree Of Life ◽  
Temporal Information ◽  
Molecular Dating ◽  
Critical Nodes ◽  
Molecular Divergence ◽  
Divergence Dates ◽  
Divergence Estimates ◽  
Age Estimates

Major disparities are recognized between molecular divergence dates and fossil ages for critical nodes in the Tree of Life, but broad patterns and underlying drivers remain elusive. We harvested 458 molecular age estimates for the stem and crown divergences of 67 avian clades to explore empirical patterns between these alternate sources of temporal information. These divergence estimates were, on average, over twice the age of the oldest fossil in these clades. Mitochondrial studies yielded older ages than nuclear studies for the vast majority of clades. Unexpectedly, disparity between molecular estimates and the fossil record was higher for divergences within major clades (crown divergences) than divergences between major clades (stem divergences). Comparisons of dates from studies classed by analytical methods revealed few significant differences. Because true divergence ages can never be known with certainty, our study does not answer the question of whether fossil gaps or molecular dating error account for a greater proportion of observed disparity. However, empirical patterns observed here suggest systemic overestimates for shallow nodes in existing molecular divergence dates for birds. We discuss underlying biases that may drive these patterns.

scholarly journals Reliable confidence intervals for RelTime estimates of evolutionary divergence times

2019 ◽  
Author(s):  
Qiqing Tao ◽  
Koichiro Tamura ◽  
Beatriz Mello ◽  
Sudhir Kumar
Keyword(s):  
Confidence Intervals ◽  
Divergence Time ◽  
Simulated Data ◽  
Molecular Dating ◽  
Divergence Times ◽  
Rate Variation ◽  
Evolutionary Divergence ◽  
Posterior Density ◽  
Divergence Time Estimates ◽  
Highest Posterior Density

AbstractConfidence intervals (CIs) depict the statistical uncertainty surrounding evolutionary divergence time estimates. They capture variance contributed by the finite number of sequences and sites used in the alignment, deviations of evolutionary rates from a strict molecular clock in a phylogeny, and uncertainty associated with clock calibrations. Reliable tests of biological hypotheses demand reliable CIs. However, current non-Bayesian methods may produce unreliable CIs because they do not incorporate rate variation among lineages and interactions among clock calibrations properly. Here, we present a new analytical method to calculate CIs of divergence times estimated using the RelTime method, along with an approach to utilize multiple calibration uncertainty densities in these analyses. Empirical data analyses showed that the new methods produce CIs that overlap with Bayesian highest posterior density (HPD) intervals. In the analysis of computer-simulated data, we found that RelTime CIs show excellent average coverage probabilities, i.e., the true time is contained within the CIs with a 95% probability. These developments will encourage broader use of computationally-efficient RelTime approach in molecular dating analyses and biological hypothesis testing.

A Transitional-Combinational Theory for the Origin of Angiosperms

Taxon ◽  
2004 ◽  
Vol 53 (1) ◽  
pp. 3 ◽  
Author(s):  
Tod F. Stuessy
Keyword(s):  
Origin Of Angiosperms
Sign in / Sign up

Export Citation Format

Share Document