The Molecular Clock and Evolutionary Rates Across the Tree of Life

Ho, Simon Y. W.

doi:10.1007/978-3-030-60181-2_1

Cited by 14 publications

(10 citation statements)

References 167 publications

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“…Over the past two decades, a number of relaxed-clock models have been developed for dating divergence events on phylogenies, allowing the substitution rate to change over time and among branches of the phylogeny; see Yang (2014 , Chapter 10) and Ho (2022) for comprehensive reviews. Thorne et al (1998) and Kishino et al (2001) developed the earliest models, using geometric Brownian motion (GBM) to describe the evolution in the rate of molecular evolution; in other words, the logarithm of the rate drifts over time like Brownian motion.…”

Section: Introductionmentioning

confidence: 99%

“…Later developments include the use of dated fossils and joint analysis of morphological characters and molecular alignments in the so-called tip-dating or total-evidence dating analyses (e.g., Ronquist et al 2012 ; Heath et al 2014 ; Zhang et al 2016 ; Alvarez-Carretero et al 2019 ). See dos Reis et al (2016) , Lee and Ho (2016) and Ho (2022) for recent reviews.…”

Section: Introductionmentioning

confidence: 99%

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Bayesian Phylogenetic Inference using Relaxed-clocks and the Multispecies Coalescent

Flouri

Huang

Jiao

et al. 2022

Molecular Biology and Evolution

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The multispecies coalescent (MSC) model accommodates both species divergences and within-species coalescent and provides a natural framework for phylogenetic analysis of genomic data when the gene trees vary across the genome. The MSC model implemented in the program bpp assumes a molecular clock and the Jukes–Cantor model, and is suitable for analyzing genomic data from closely related species. Here we extend our implementation to more general substitution models and relaxed clocks to allow the rate to vary among species. The MSC-with-relaxed-clock model allows the estimation of species divergence times and ancestral population sizes using genomic sequences sampled from contemporary species when the strict clock assumption is violated, and provides a simulation framework for evaluating species tree estimation methods. We conducted simulations and analyzed two real datasets to evaluate the utility of the new models. We confirm that the clock-JC model is adequate for inference of shallow trees with closely related species, but it is important to account for clock violation for distant species. Our simulation suggests that there is valuable phylogenetic information in the gene-tree branch lengths even if the molecular clock assumption is seriously violated, and the relaxed-clock models implemented in bpp are able to extract such information. Our Markov chain Monte Carlo algorithms suffer from mixing problems when used for species tree estimation under the relaxed clock and we discuss possible improvements. We conclude that the new models are currently most effective for estimating population parameters such as species divergence times when the species tree is fixed.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Bayesian Phylogenetic Inference using Relaxed-clocks and the Multispecies Coalescent

Flouri

Huang

Jiao

et al. 2022

Molecular Biology and Evolution

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“…It has also been suggested that biotic drivers play a major role in the expansion phase, whereas abiotic drivers are more influential in the retraction phase [ 29 ]. In all these works, the duration of taxon cycles was deduced from phylogenetic divergence times, which are usually estimated using molecular clock assumptions or are modeled using a variety of indirect methods [ 30 ]. Therefore, phylogenetic divergence times are hypotheses, not empirical evidence [ 31 ].…”

Section: Introductionmentioning

confidence: 99%

Taxon Cycles in Neotropical Mangroves

Rull

2023

Plants

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The concept of the taxon cycle involves successive range expansions and contractions over time, through which a species can indefinitely maintain its core distribution. Otherwise, it becomes extinct. Taxon cycles have been defined mostly for tropical island faunas; examples from continental areas are scarce, and similar case studies for plants remain unknown. Most taxon cycles have been identified on the basis of phylogeographic studies, and straightforward empirical evidence from fossils is lacking. Here, empirical fossil evidence is provided for the recurrent Eocene to the present expansion/contraction cycles in a mangrove taxon (Pelliciera) after a Neotropical-wide study of the available pollen records. This recurrent behavior is compatible with the concept of the taxon cycle from biogeographical, chronological and ecological perspectives. The biotic and abiotic drivers potentially involved in the initiation and maintenance of the Pelliciera expansion/contraction cycles are analyzed, and the ecological and evolutionary implications are discussed. Whether this could be a trend toward extinction is considered under the predictions of the taxon cycle theory. The recurrent expansion and contraction cycles identified for Pelliciera have strong potential for being the first empirically and unequivocally documented taxon cycles and likely the only taxon cycles documented to date for plants.

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“…Several factors can contribute to TDRP such as incomplete purifying selection [6,7], accelerated evolution upon introduction to a new host environment [8,9], and site substitution saturation [2,10]. In addition to these biological processes, several other factors such as misspecification of substitution models can also contribute to time-dependent changes in the evolutionary rate estimates [11]. In a recent work [10], a mechanistic evolutionary model, also known as the Prisoner of War (PoW) model, was proposed that readily explains and corrects for time-dependent rate effects across deep evolutionary timescales and reproduces the empirically observed power-law rate decay found for RNA and DNA viruses.…”

Section: Introductionmentioning

confidence: 99%

Revisiting the origins of theSobemovirusgenus: a case for ancient origins of plant viruses

Ghafari,

Somera,

Sarmiento

et al. 2023

Preprint

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The discrepancy between short- and long-term rate estimates, known as the time-dependent rate phenomenon (TDRP), poses a challenge to extrapolating evolutionary rates over time and reconstructing evolutionary history of viruses. The TDRP reveals a decline in evolutionary rate estimates with the measurement timescale, explained empirically by a power-law rate decay, notably observed in animal and human viruses. A mechanistic evolutionary model, the Prisoner of War (PoW) model, has been proposed to address TDRP in viruses. Although TDRP has been studied in animal viruses, its impact on plant virus evolutionary history remains largely unexplored. Here, we investigated the consequences of TDRP in plant viruses by applying the PoW model to reconstruct the evolutionary history of sobemoviruses, plant pathogens with significant importance due to their impact on agriculture and plant health. Our analysis showed that theSobemovirusgenus dates back over four million years, indicating an ancient origin. We found evidence that supports deep host jumps to Poaceae, Fabaceae, and Solanaceae occurring between tens to hundreds of thousand years ago, followed by specialization. Remarkably, the TDRP-corrected evolutionary history of sobemoviruses was extended far beyond previous estimates that had suggested their emergence during the Neolithic period. By incorporating sequences collected through metagenomic analyses, the resulting phylogenetic tree showcases increased genetic diversity, reflecting a deep history of sobemovirus species with major radiation events taking place during the Neolithic period, suggesting rapid diversification in that period. Our findings make a case for the possibility of deep evolutionary origins of plant viruses.

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The Molecular Clock and Evolutionary Rates Across the Tree of Life

Cited by 14 publications

References 167 publications

Bayesian Phylogenetic Inference using Relaxed-clocks and the Multispecies Coalescent

Bayesian Phylogenetic Inference using Relaxed-clocks and the Multispecies Coalescent

Taxon Cycles in Neotropical Mangroves

Revisiting the origins of theSobemovirusgenus: a case for ancient origins of plant viruses

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