scholarly journals Divergence time of the two regional medaka populations in Japan as a new time scale for comparative genomics of vertebrates

2009 ◽  
Vol 5 (6) ◽  
pp. 812-816 ◽  
Author(s):  
Davin H. E. Setiamarga ◽  
Masaki Miya ◽  
Yusuke Yamanoue ◽  
Yoichiro Azuma ◽  
Jun G. Inoue ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Molecular Clock ◽  
Divergence Time ◽  
Evolutionary Rates ◽  
Implicit Assumption ◽  
Molecular Evolutionary Rates ◽  
Clock Analysis ◽  
The Japanese Archipelago ◽  
Two Populations ◽  
Rates Of Molecular Evolution

The southern and northern Japanese populations of the medaka fish provide useful tools to gain insights into the comparative genomics and speciation of vertebrates, because they can breed to produce healthy and fertile offspring despite their highly divergent genetic backgrounds compared with those of human–chimpanzee. Comparative genomics analysis has suggested that such large genetic differences between the two populations are caused by higher molecular evolutionary rates among the medakas than those of the hominids. The argument, however, was based on the assumption that the two Japanese populations diverged approximately at the same time (4.0–4.7 Myr ago) as the human–chimpanzee lineage (5.0–6.0 Myr ago). This can be misleading, because the divergence time of the two populations was calculated based on estimated, extremely higher molecular evolutionary rates of other fishes with an implicit assumption of a global molecular clock. Here we show that our estimate, based on a Bayesian relaxed molecular-clock analysis of whole mitogenome sequences from 72 ray-finned fishes (including 14 medakas), is about four times older than that of the previous study (18 Myr). This remarkably older estimate can be reconciled with the vicariant events of the Japanese archipelago, and the resulting rates of molecular evolution are almost identical between the medaka and hominid lineages. Our results further highlight the fact that reproductive isolation may not evolve despite a long period of geographical isolation.

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 Gene diversity in finite populations

1985 ◽  
Vol 46 (1) ◽  
pp. 107-113 ◽  
Author(s):  
Naoyuki Takahata
Keyword(s):  
Genetic Variation ◽  
Dna Sequence ◽  
Molecular Clock ◽  
Sequence Comparison ◽  
Gene Diversity ◽  
Divergence Time ◽  
Homologous Genes ◽  
Stochastic Forces ◽  
Two Populations ◽  
Dna Sequence Comparison

DNA sequence comparison among homologous genes sampled at random from one or two populations allows one to estimate the ultimate amount of genetic variation maintained in a population and to construct the gene genealogy within and between populations. Moreover, if we use the finding of the molecular clock (Zuckerkandl & Pauling, 1965), it is also possible to estimate the divergence time of populations examined. Such an estimated divergence time is, however, intricately affected by samples and stochastic forces occurring in the course of evolution.

scholarly journals Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil

Science ◽  
2021 ◽  
pp. eabh2644 ◽  
Author(s):  
Nuno R. Faria ◽  
Thomas A. Mellan ◽  
Charles Whittaker ◽  
Ingra M. Claro ◽  
Darlan da S. Candido ◽  
...  
Keyword(s):  
Molecular Evolution ◽  
Genome Sequencing ◽  
Immune Evasion ◽  
Molecular Clock ◽  
Spike Protein ◽  
Dynamical Model ◽  
Mortality Data ◽  
Clock Analysis ◽  
Protection Against Infection ◽  
Molecular Clock Analysis

Cases of SARS-CoV-2 infection in Manaus, Brazil, resurged in late 2020, despite previously high levels of infection. Genome sequencing of viruses sampled in Manaus between November 2020 and January 2021 revealed the emergence and circulation of a novel SARS-CoV-2 variant of concern. Lineage P.1, acquired 17 mutations, including a trio in the spike protein (K417T, E484K and N501Y) associated with increased binding to the human ACE2 receptor. Molecular clock analysis shows that P.1 emergence occurred around mid-November 2020 and was preceded by a period of faster molecular evolution. Using a two-category dynamical model that integrates genomic and mortality data, we estimate that P.1 may be 1.7–2.4-fold more transmissible, and that previous (non-P.1) infection provides 54–79% of the protection against infection with P.1 that it provides against non-P.1 lineages. Enhanced global genomic surveillance of variants of concern, which may exhibit increased transmissibility and/or immune evasion, is critical to accelerate pandemic responsiveness.

scholarly journals Understanding the Overdispersed Molecular Clock

Genetics ◽  
2000 ◽  
Vol 154 (3) ◽  
pp. 1403-1417 ◽  
Author(s):  
David J Cutler
Keyword(s):  
Molecular Evolution ◽  
Molecular Clock ◽  
Time Scale ◽  
Population Parameter ◽  
Deleterious Mutations ◽  
Slow Time ◽  
Slow Time Scale ◽  
Key Population ◽  
Protein Encoding ◽  
Rates Of Molecular Evolution

Abstract Rates of molecular evolution at some protein-encoding loci are more irregular than expected under a simple neutral model of molecular evolution. This pattern of excessive irregularity in protein substitutions is often called the “overdispersed molecular clock” and is characterized by an index of dispersion, R(T) > 1. Assuming infinite sites, no recombination model of the gene R(T) is given for a general stationary model of molecular evolution. R(T) is shown to be affected by only three things: fluctuations that occur on a very slow time scale, advantageous or deleterious mutations, and interactions between mutations. In the absence of interactions, advantageous mutations are shown to lower R(T); deleterious mutations are shown to raise it. Previously described models for the overdispersed molecular clock are analyzed in terms of this work as are a few very simple new models. A model of deleterious mutations is shown to be sufficient to explain the observed values of R(T). Our current best estimates of R(T) suggest that either most mutations are deleterious or some key population parameter changes on a very slow time scale. No other interpretations seem plausible. Finally, a comment is made on how R(T) might be used to distinguish selective sweeps from background selection.

scholarly journals Multiple transgressions and slow evolution shape the phylogeographic pattern of the blind cave-dwelling shrimp Typhlocaris

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5268 ◽  
Author(s):  
Tamar Guy-Haim ◽  
Noa Simon-Blecher ◽  
Amos Frumkin ◽  
Israel Naaman ◽  
Yair Achituv
Keyword(s):  
Molecular Evolution ◽  
Mediterranean Sea ◽  
Divergence Time ◽  
Evolutionary Rates ◽  
Radiometric Dating ◽  
Small Range ◽  
Biogeographic Patterns ◽  
Blind Cave ◽  
The Mediterranean ◽  
Slow Evolution

Background Aquatic subterranean species often exhibit disjunct distributions, with high level of endemism and small range, shaped by vicariance, limited dispersal, and evolutionary rates. We studied the disjunct biogeographic patterns of an endangered blind cave shrimp, Typhlocaris, and identified the geological and evolutionary processes that have shaped its divergence pattern. Methods We collected Typlocaris specimens of three species (T. galilea, T. ayyaloni, and T. salentina), originating from subterranean groundwater caves by the Mediterranean Sea, and used three mitochondrial genes (12S, 16S, cytochrome oxygnese subunit 1 (COI)) and four nuclear genes (18S, 28S, internal transcribed spacer, Histon 3) to infer their phylogenetic relationships. Using the radiometric dating of a geological formation (Bira) as a calibration node, we estimated the divergence times of the Typhlocaris species and the molecular evolution rates. Results The multi-locus ML/Bayesian trees of the concatenated seven gene sequences showed that T. salentina (Italy) and T. ayyaloni (Israel) are sister species, both sister to T. galilea (Israel). The divergence time of T. ayyaloni and T. salentina from T. galilea was 7.0 Ma based on Bira calibration. The divergence time of T. ayyaloni from T. salentina was 5.7 (4.4–6.9) Ma according to COI, and 5.8 (3.5–7.2) Ma according to 16S. The computed interspecific evolutionary rates were 0.0077 substitutions/Myr for COI, and 0.0046 substitutions/Myr for 16S. Discussion Two consecutive vicariant events have shaped the phylogeographic patterns of Typhlocaris species. First, T. galilea was tectonically isolated from its siblings in the Mediterranean Sea by the arching uplift of the central mountain range of Israel ca. seven Ma. Secondly, T. ayyaloni and T. salentina were stranded and separated by a marine transgression ca. six Ma, occurring just before the Messinian Salinity Crisis. Our estimated molecular evolution rates were in one order of magnitude lower than the rates of closely related crustaceans, as well as of other stygobiont species. We suggest that this slow evolution reflects the ecological conditions prevailing in the highly isolated subterranean water bodies inhabited by Typhlocaris.

Evolutionary Analyses of Protein Interaction Networks

2009 ◽  
pp. 169-181 ◽  
Author(s):  
Takashi Makino ◽  
Aoife McLysaght
Keyword(s):  
Molecular Evolution ◽  
Comparative Genomics ◽  
Protein Interaction ◽  
Protein Interaction Networks ◽  
Evolutionary Rates ◽  
Interaction Networks ◽  
Evolutionary Mechanisms ◽  
Ancestral Gene ◽  
Protein Protein Interaction ◽  
A Genome

This chapter introduces evolutionary analyses of protein interaction networks and of proteins as components of the networks. The authors show relationships between proteins in the networks and their evolutionary rates. For understanding protein-protein interaction (PPI) divergence, duplicated genes are often compared because they are derived from a common ancestral gene. In order to reveal evolutionary mechanisms acting on the interactome it is necessary to compare PPIs across species. Investigation of co-localization of interacting genes in a genome shows that PPIs have an important role in the maintenance of a physical link between neighboring genes. The purpose of this chapter is to introduce methodologies for analyzing PPI data and to describe molecular evolution and comparative genomics insights gained from such studies.

scholarly journals Evolutionary rates of mitochondrial genomes correspond to diversification rates and to contemporary species richness in birds and reptiles

2010 ◽  
Vol 277 (1700) ◽  
pp. 3587-3592 ◽  
Author(s):  
Soo Hyung Eo ◽  
J. Andrew DeWoody
Keyword(s):  
Species Richness ◽  
Nuclear Data ◽  
Synonymous Substitution ◽  
Evolutionary Rates ◽  
Rate Variation ◽  
Substitution Rates ◽  
Diversification Rates ◽  
Extinction Process ◽  
Molecular Evolutionary Rates ◽  
Speciation Rates

Rates of biological diversification should ultimately correspond to rates of genome evolution. Recent studies have compared diversification rates with phylogenetic branch lengths, but incomplete phylogenies hamper such analyses for many taxa. Herein, we use pairwise comparisons of confamilial sauropsid (bird and reptile) mitochondrial DNA (mtDNA) genome sequences to estimate substitution rates. These molecular evolutionary rates are considered in light of the age and species richness of each taxonomic family, using a random-walk speciation–extinction process to estimate rates of diversification. We find the molecular clock ticks at disparate rates in different families and at different genes. For example, evolutionary rates are relatively fast in snakes and lizards, intermediate in crocodilians and slow in turtles and birds. There was also rate variation across genes, where non-synonymous substitution rates were fastest at ATP8 and slowest at CO 3. Family-by-gene interactions were significant, indicating that local clocks vary substantially among sauropsids. Most importantly, we find evidence that mitochondrial genome evolutionary rates are positively correlated with speciation rates and with contemporary species richness. Nuclear sequences are poorly represented among reptiles, but the correlation between rates of molecular evolution and species diversification also extends to 18 avian nuclear genes we tested. Thus, the nuclear data buttress our mtDNA findings.

Wing shape and environmental energy are associated with molecular evolutionary rates in a large avian radiation

2020 ◽  
Author(s):  
David Alejandro Duchêne ◽  
Paola Montoya ◽  
Carlos Daniel Cadena
Keyword(s):  
Uv Radiation ◽  
Positive Association ◽  
Evolutionary Rates ◽  
Wing Morphology ◽  
Geographic Ranges ◽  
Molecular Evolutionary Rates ◽  
Strong Positive Association ◽  
Genomic Regions ◽  
Avian Family

AbstractAmong the macroevolutionary drivers of molecular evolutionary rates, metabolic demands and environmental energy have been a central topic of discussion. The large number of studies examining these associations have found mixed results, and have rarely explored the interactions among various factors impacting molecular evolutionary rates. Taking the diverse avian family Furnariidae as a case study, we examined the association between several estimates of molecular evolutionary rates with a proxy of metabolic demands imposed by flight (wing morphology) and proxies of environmental energy across the geographic ranges of species (temperature and UV radiation). We found a strong positive association between molecular rates in genomic regions that can change the coded amino-acid with wing morphology, environmental temperature, and UV radiation. Strikingly, however, we did not find evidence of such associations with molecular rates at sites not impacting amino-acids. Our results suggest that the demands of flight and environmental energy primarily impact genome evolution by placing selective constraints, instead of being associated with basal mutation rates.

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