scholarly journals The molecular clock as a tool for understanding host-parasite evolution

2020 ◽  
Author(s):  
Rachel Warnock ◽  
Jan Engelstädter
Keyword(s):  
Molecular Clock ◽  
Divergence Time ◽  
Time Estimation ◽  
Bayesian Approaches ◽  
Deep Time ◽  
Geological Evidence ◽  
Divergence Time Estimation ◽  
Fossil Records ◽  
Host Parasite ◽  
Alpha Proteobacteria

The molecular clock in combination with evidence from the geological record can be applied to infer the timing and dynamics of evolutionary events. This has enormous potential to shed light on the complex and often evasive evolution of parasites. Here, we provide an overview of molecular clock methodology and recent advances that increase the potential for the study of host-parasite coevolutionary dynamics, with a focus on Bayesian approaches to divergence time estimation. We highlight the challenges in applying these methods to the study of parasites, including the nature of parasite genomes, the incompleteness of the rock and fossil records, and the complexity of host-parasite interactions. Developments in models of molecular evolution and approaches to deriving temporal constraints from geological evidence will help overcome some of these issues. However, we also describe a case study in which the timescale of host-parasite coevolution cannot easily be inferred using existing methods – that of the alpha-proteobacteria Wolbachia. We conclude by providing a prospective on future methodological developments and data collection that will facilitate in understanding the role of parasitism in deep time.

scholarly journals Exploring uncertainty in the calibration of the molecular clock

2011 ◽  
Vol 8 (1) ◽  
pp. 156-159 ◽  
Author(s):  
Rachel C. M. Warnock ◽  
Ziheng Yang ◽  
Philip C. J. Donoghue
Keyword(s):  
Molecular Clock ◽  
Divergence Time ◽  
Time Estimation ◽  
Divergence Times ◽  
Bayesian Approaches ◽  
Divergence Time Estimation ◽  
Clock Analysis ◽  
True Time ◽  
Time Of Divergence ◽  
The Impact

Calibration is a critical step in every molecular clock analysis but it has been the least considered. Bayesian approaches to divergence time estimation make it possible to incorporate the uncertainty in the degree to which fossil evidence approximates the true time of divergence. We explored the impact of different approaches in expressing this relationship, using arthropod phylogeny as an example for which we established novel calibrations. We demonstrate that the parameters distinguishing calibration densities have a major impact upon the prior and posterior of the divergence times, and it is critically important that users evaluate the joint prior distribution of divergence times used by their dating programmes. We illustrate a procedure for deriving calibration densities in Bayesian divergence dating through the use of soft maximum constraints.

scholarly journals Divergence time estimation of Galliformes based on the best gene shopping scheme of ultraconserved elements

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
De Chen ◽  
Peter A. Hosner ◽  
Donna L. Dittmann ◽  
John P. O’Neill ◽  
Sharon M. Birks ◽  
...  
Keyword(s):  
Divergence Time ◽  
Time Estimation ◽  
Molecular Dating ◽  
Great Promise ◽  
Data Types ◽  
Ultraconserved Elements ◽  
Divergence Time Estimation ◽  
Dating Methods ◽  
Data Heterogeneity ◽  
Fossil Records

Abstract Background Divergence time estimation is fundamental to understanding many aspects of the evolution of organisms, such as character evolution, diversification, and biogeography. With the development of sequence technology, improved analytical methods, and knowledge of fossils for calibration, it is possible to obtain robust molecular dating results. However, while phylogenomic datasets show great promise in phylogenetic estimation, the best ways to leverage the large amounts of data for divergence time estimation has not been well explored. A potential solution is to focus on a subset of data for divergence time estimation, which can significantly reduce the computational burdens and avoid problems with data heterogeneity that may bias results. Results In this study, we obtained thousands of ultraconserved elements (UCEs) from 130 extant galliform taxa, including representatives of all genera, to determine the divergence times throughout galliform history. We tested the effects of different “gene shopping” schemes on divergence time estimation using a carefully, and previously validated, set of fossils. Our results found commonly used clock-like schemes may not be suitable for UCE dating (or other data types) where some loci have little information. We suggest use of partitioning (e.g., PartitionFinder) and selection of tree-like partitions may be good strategies to select a subset of data for divergence time estimation from UCEs. Our galliform time tree is largely consistent with other molecular clock studies of mitochondrial and nuclear loci. With our increased taxon sampling, a well-resolved topology, carefully vetted fossil calibrations, and suitable molecular dating methods, we obtained a high quality galliform time tree. Conclusions We provide a robust galliform backbone time tree that can be combined with more fossil records to further facilitate our understanding of the evolution of Galliformes and can be used as a resource for comparative and biogeographic studies in this group.

Divergence time estimation in Cichorieae (Asteraceae) using a fossil-calibrated relaxed molecular clock

2012 ◽  
Vol 13 (1) ◽  
pp. 1-13 ◽  
Author(s):  
Karin Tremetsberger ◽  
Birgit Gemeinholzer ◽  
Holger Zetzsche ◽  
Stephen Blackmore ◽  
Norbert Kilian ◽  
...  
Keyword(s):  
Molecular Clock ◽  
Divergence Time ◽  
Time Estimation ◽  
Divergence Time Estimation ◽  
Relaxed Molecular Clock

scholarly journals Performance of A Priori and A Posteriori Calibration Strategies in Divergence Time Estimation

2020 ◽  
Vol 12 (7) ◽  
pp. 1087-1098
Author(s):  
Alan J S Beavan ◽  
Philip C J Donoghue ◽  
Mark A Beaumont ◽  
Davide Pisani
Keyword(s):  
Molecular Clock ◽  
A Priori ◽  
Divergence Time ◽  
Time Estimation ◽  
Branch Length ◽  
Divergence Times ◽  
A Posteriori ◽  
Geological Time ◽  
Divergence Time Estimation ◽  
Relative Divergence

Abstract Relaxed molecular clock methods allow the use of genomic data to estimate divergence times across the tree of life. This is most commonly achieved in Bayesian analyses where the molecular clock is calibrated a priori through the integration of fossil information. Alternatively, fossil calibrations can be used a posteriori, to transform previously estimated relative divergence times that were inferred without considering fossil information, into absolute divergence times. However, as branch length is the product of the rate of evolution and the duration in time of the considered branch, the extent to which a posteriori calibrated, relative divergence time methods can disambiguate time and rate, is unclear. Here, we use forward evolutionary simulations and compare a priori and a posteriori calibration strategies using different molecular clock methods and models. Specifically, we compare three Bayesian methods, the strict clock, uncorrelated clock and autocorrelated clock, and the non-Bayesian algorithm implemented in RelTime. We simulate phylogenies with multiple, independent substitution rate changes and show that correct timescales cannot be inferred without the use of calibrations. Under our simulation conditions, a posteriori calibration strategies almost invariably inferred incorrect rate changes and divergence times. The a priori integration of fossil calibrations is fundamental in these cases to improve the accuracy of the estimated divergence times. Relative divergence times and absolute timescales derived by calibrating relative timescales to geological time a posteriori appear to be less reliable than a priori calibrated, timescales.

scholarly journals Paleogenomics of echinoids reveals an ancient origin for the double-negative specification of micromeres in sea urchins

2017 ◽  
Vol 114 (23) ◽  
pp. 5870-5877 ◽  
Author(s):  
Jeffrey R. Thompson ◽  
Eric M. Erkenbrack ◽  
Veronica F. Hinman ◽  
Brenna S. McCauley ◽  
Elizabeth Petsios ◽  
...  
Keyword(s):  
Developmental Biology ◽  
Regulatory Networks ◽  
Sea Urchins ◽  
Divergence Time ◽  
Time Estimation ◽  
Late Triassic ◽  
Ancestral State ◽  
Double Negative ◽  
Deep Time ◽  
Divergence Time Estimation

Establishing a timeline for the evolution of novelties is a common, unifying goal at the intersection of evolutionary and developmental biology. Analyses of gene regulatory networks (GRNs) provide the ability to understand the underlying genetic and developmental mechanisms responsible for the origin of morphological structures both in the development of an individual and across entire evolutionary lineages. Accurately dating GRN novelties, thereby establishing a timeline for GRN evolution, is necessary to answer questions about the rate at which GRNs and their subcircuits evolve, and to tie their evolution to paleoenvironmental and paleoecological changes. Paleogenomics unites the fossil record and all aspects of deep time, with modern genomics and developmental biology to understand the evolution of genomes in evolutionary time. Recent work on the regulatory genomic basis of development in cidaroid echinoids, sand dollars, heart urchins, and other nonmodel echinoderms provides an ideal dataset with which to explore GRN evolution in a comparative framework. Using divergence time estimation and ancestral state reconstructions, we have determined the age of the double-negative gate (DNG), the subcircuit which specifies micromeres and skeletogenic cells in Strongylocentrotus purpuratus. We have determined that the DNG has likely been used for euechinoid echinoid micromere specification since at least the Late Triassic. The innovation of the DNG thus predates the burst of post-Paleozoic echinoid morphological diversification that began in the Early Jurassic. Paleogenomics has wide applicability for the integration of deep time and molecular developmental data, and has wide utility in rigorously establishing timelines for GRN evolution.

scholarly journals Out of the Qinghai-Tibetan Plateau (QTP) and rapid radiation across Eurasia for Allium section Daghestanica (Amaryllidaceae)

AoB Plants ◽  
2021 ◽  
Author(s):  
Min-Jie Li ◽  
Huan-Xi Yu ◽  
Xian-Lin Guo ◽  
Xing-Jin He
Keyword(s):  
Evolutionary History ◽  
Divergence Time ◽  
Time Estimation ◽  
Adjacent Region ◽  
Rapid Radiation ◽  
Divergence Time Estimation ◽  
Species Diversification ◽  
The Third ◽  
Evolutionary Line ◽  
History Of

Abstract The disjunctive distribution (Europe-Caucasus-Asia) and species diversification across Eurasia for the genus Allium sect. Daghestanica has fascinating attractions for researchers aiming to understanding the development and history of the modern Eurasia flora. However, no any studies have been carried out to address the evolutionary history of this section. Based on the nrITS and cpDNA fragments (trnL-trnF and rpl32-trnL), the evolutionary history of the third evolutionary line (EL3) of the genus Allium was reconstructed and we further elucidate the evolutionary line of sect. Daghestanica under this background. Our molecular phylogeny recovered two highly supported clades in sect. Daghestanica: the Clade I includes Caucasian-European species and Asian A. maowenense, A. xinlongense and A. carolinianum collected in Qinghai; the Clade II comprises Asian yellowish tepal species, A. chrysanthum, A. chrysocephalum, A. herderianum, A. rude and A. xichuanense. The divergence time estimation and biogeography inference indicated that Asian ancestor located in the QTP and the adjacent region could have migrated to Caucasus and Europe distributions around the Late Miocene and resulted in further divergence and speciation; Asian ancestor underwent the rapid radiation in the QTP and the adjacent region most likely due to the heterogeneous ecology of the QTP resulted from the orogeneses around 4–3 Mya. Our study provides a picture to understand the origin and species diversification across Eurasia for sect. Daghestanica.

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