scholarly journals Regional effect on the molecular clock rate of protein evolution in Eutherian and Metatherian genomes

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Raf Huttener ◽  
Lieven Thorrez ◽  
Thomas in‘t Veld ◽  
Barney Potter ◽  
Guy Baele ◽  
...  
Keyword(s):  
Protein Evolution ◽  
Molecular Clock ◽  
Clock Rate ◽  
Regional Effect ◽  
Sliding Windows ◽  
Protein Divergence ◽  
Regional Effects ◽  
Specific Effects ◽  
A Genome ◽  
Phylogenetic Lineages

Abstract Background Different types of proteins diverge at vastly different rates. Moreover, the same type of protein has been observed to evolve with different rates in different phylogenetic lineages. In the present study we measured the rates of protein evolution in Eutheria (placental mammals) and Metatheria (marsupials) on a genome-wide basis and we propose that the gene position in the genome landscape has an important influence on the rate of protein divergence. Results We analyzed a protein-encoding gene set (n = 15,727) common to 16 mammals (12 Eutheria and 4 Metatheria). Using sliding windows that averaged regional effects of protein divergence we constructed landscapes in which strong and lineage-specific regional effects were seen on the molecular clock rate of protein divergence. Within each lineage, the relatively high rates were preferentially found in subtelomeric chromosomal regions. Such regions were observed to contain important and well-studied loci for fetal growth, uterine function and the generation of diversity in the adaptive repertoire of immunoglobulins. Conclusions A genome landscape approach visualizes lineage-specific regional differences between Eutherian and Metatherian rates of protein evolution. This phenomenon of chromosomal position is a new element that explains at least part of the lineage-specific effects and differences between proteins on the molecular clock rates.

scholarly journals Mitochondria-encoded genes contribute to evolution of heat and cold tolerance in yeast

2019 ◽  
Vol 5 (1) ◽  
pp. eaav1848 ◽  
Author(s):  
Xueying C. Li ◽  
David Peris ◽  
Chris Todd Hittinger ◽  
Elaine A. Sia ◽  
Justin C. Fay
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Cold Tolerance ◽  
Yeast Species ◽  
Saccharomyces Uvarum ◽  
Phenotypic Differences ◽  
Protein Divergence ◽  
Thermal Growth ◽  
Genome Wide ◽  
A Genome ◽  
Moderate Effect

Genetic analysis of phenotypic differences between species is typically limited to interfertile species. Here, we conducted a genome-wide noncomplementation screen to identify genes that contribute to a major difference in thermal growth profile between two reproductively isolated yeast species,Saccharomyces cerevisiaeandSaccharomyces uvarum. The screen identified only a single nuclear-encoded gene with a moderate effect on heat tolerance, but, in contrast, revealed a large effect of mitochondrial DNA (mitotype) on both heat and cold tolerance. Recombinant mitotypes indicate that multiple genes contribute to thermal divergence, and we show that protein divergence inCOX1affects both heat and cold tolerance. Our results point to the yeast mitochondrial genome as an evolutionary hotspot for thermal divergence.

INEQUALITY, FDI AND ECONOMIC DEVELOPMENT: EVIDENCE FROM DEVELOPING COUNTRIES

2017 ◽  
Vol 62 (05) ◽  
pp. 1039-1057 ◽  
Author(s):  
MUHAMMAD TARIQ MAJEED
Keyword(s):  
Economic Development ◽  
Estimation Methods ◽  
Host Countries ◽  
Data Set ◽  
Regional Effects ◽  
Specific Effects ◽  
Level Of Economic Development ◽  
Time Specific ◽  
High Level ◽  
The Impact

This paper empirically investigates the impact of Foreign Direct Investment (FDI) on inequality using a panel data set of 65 developing counties. While the existing literature mainly examines the impact of FDI on growth, this study explores the importance of domestic conditions of the host countries in determining the distributional effects of FDI. The results show that the impact of FDI is not homogenous on host countries as FDI inflows exert inequality-narrowing effect only in countries that have stronger investment in human capital, better financial sector and a high level of economic development. While FDI accentuates not ameliorates inequality in countries with low level of economic development, findings of the study are robust to the use of different specifications, different estimation methods, inclusion of regional effects and time specific effects.

scholarly journals Complete Genomic Sequence of Human Coronavirus OC43: Molecular Clock Analysis Suggests a Relatively Recent Zoonotic Coronavirus Transmission Event

2005 ◽  
Vol 79 (3) ◽  
pp. 1595-1604 ◽  
Author(s):  
Leen Vijgen ◽  
Els Keyaerts ◽  
Elien Moës ◽  
Inge Thoelen ◽  
Elke Wollants ◽  
...  
Keyword(s):  
Molecular Clock ◽  
Complete Genome ◽  
Recent Common Ancestor ◽  
Human Coronavirus ◽  
Transmission Event ◽  
Most Recent Common Ancestor ◽  
A Genome ◽  
Clock Analysis ◽  
Group 2 ◽  
Molecular Clock Analysis

ABSTRACT Coronaviruses are enveloped, positive-stranded RNA viruses with a genome of approximately 30 kb. Based on genetic similarities, coronaviruses are classified into three groups. Two group 2 coronaviruses, human coronavirus OC43 (HCoV-OC43) and bovine coronavirus (BCoV), show remarkable antigenic and genetic similarities. In this study, we report the first complete genome sequence (30,738 nucleotides) of the prototype HCoV-OC43 strain (ATCC VR759). Complete genome and open reading frame (ORF) analyses were performed in comparison to the BCoV genome. In the region between the spike and membrane protein genes, a 290-nucleotide deletion is present, corresponding to the absence of BCoV ORFs ns4.9 and ns4.8. Nucleotide and amino acid similarity percentages were determined for the major HCoV-OC43 ORFs and for those of other group 2 coronaviruses. The highest degree of similarity is demonstrated between HCoV-OC43 and BCoV in all ORFs with the exception of the E gene. Molecular clock analysis of the spike gene sequences of BCoV and HCoV-OC43 suggests a relatively recent zoonotic transmission event and dates their most recent common ancestor to around 1890. An evolutionary rate in the order of 4 × 10−4 nucleotide changes per site per year was estimated. This is the first animal-human zoonotic pair of coronaviruses that can be analyzed in order to gain insights into the processes of adaptation of a nonhuman coronavirus to a human host, which is important for understanding the interspecies transmission events that led to the origin of the severe acute respiratory syndrome outbreak.

scholarly journals Frequent lineage-specific substitution rate changes support an episodic model for protein evolution

2021 ◽  
Author(s):  
Neel Prabh ◽  
Diethard Tautz
Keyword(s):  
Protein Evolution ◽  
Substitution Rate ◽  
Large Fraction ◽  
Null Model ◽  
Amino Acid Sequences ◽  
Substitution Pattern ◽  
Molecular Clock Model ◽  
Constant Change ◽  
A Genome ◽  
History Of

Abstract Since the inception of the molecular clock model for sequence evolution, the investigation of protein divergence has revolved around the question of a more or less constant change of amino acid sequences, with specific overall rates for each family. Although anomalies in clock-like divergence are well known, the assumption of a constant decay rate for a given protein family is usually taken as the null model for protein evolution. However, systematic tests of this null model at a genome-wide scale have lagged behind, despite the databases’ enormous growth. We focus here on divergence rate comparisons between very closely related lineages since this allows clear orthology assignments by synteny and reliable alignments, which are crucial for determining substitution rate changes. We generated a high-confidence dataset of syntenic orthologs from four ape species, including humans. We find that despite the appearance of an overall clock-like substitution pattern, several hundred protein families show lineage-specific acceleration and deceleration in divergence rates, or combinations of both in different lineages. Hence, our analysis uncovers a rather dynamic history of substitution rate changes, even between these closely related lineages, implying that one should expect that a large fraction of proteins will have had a history of episodic rate changes in deeper phylogenies. Furthermore, each of the lineages has a separate set of particularly fast diverging proteins. The genes with the highest percentage of branch-specific substitutions are ADCYAP1 in the human lineage (9.7%), CALU in chimpanzees (7.1%), SLC39A14 in the internal branch leading to humans and chimpanzees (4.1%), RNF128 in gorillas (9%), and S100Z in gibbons (15.2%). The mutational pattern in ADCYAP1 suggests a biased mutation process, possibly through asymmetric gene conversion effects. We conclude that a null model of constant change can be problematic for predicting the evolutionary trajectories of individual proteins.

REGIONALS AND RESIDUALS IN SEISMIC PROSPECTING FOR STRATIGRAPHIC FEATURES

Geophysics ◽  
1964 ◽  
Vol 29 (1) ◽  
pp. 38-53 ◽  
Author(s):  
M. B. Dobrin ◽  
W. G. Rimmer
Keyword(s):  
High Speed ◽  
Cross Product ◽  
Velocity Variation ◽  
Regional Effect ◽  
Oil Accumulation ◽  
Regional Effects ◽  
Regional Trends ◽  
Geological Features ◽  
Gravity And Magnetic ◽  
Processing Techniques

Many geological features associated with oil accumulation show up on seismic maps as interruptions of regional trends rather than as true structural closures. Among such features are reefs, which are often best detected by draping of overlying formations; erosional escarpments which truncate porous limestone beds on their updip sides; and buried ridges which cause productive stratigraphic buildups in overlying beds. In the presence of regional tilting, seismic indications from such features can be so obscured that special data‐processing techniques are required to make them readily recognizable on seismic maps. The problem here is very similar to that of separating gravity and magnetic effects of features having economic interest from regional background. Residual techniques developed for accomplishing this type of separation can be applied advantageously to seismic data where regional structure obscures significant anomalies. Both contour‐smoothing or grid methods can be used depending on the nature of the problem and the preference of the interpreter. As with gravity or magnetics, the grid methods are particularly adaptable for high‐speed electronic computation. Some examples are shown where regional effects are removed from seismic maps over known reefs and productive erosional escarpments by techniques using electronic computation. A somewhat different approach is necessary when it is desired to remove the effect of velocity variation from time maps by treating the velocity function as a regional effect. Here the regional is multiplicative rather than additive and cross‐product terms must be taken into account. By relating the time maps and velocity maps using this approach, the principal hazards of using time maps for interpretation can be avoided.

The Multispecies Coalescent in Space and Time

2020 ◽  
Author(s):  
Patrick F. McKenzie ◽  
Deren A. R. Eaton
Keyword(s):  
Gene Tree ◽  
Species Tree ◽  
Gene Trees ◽  
Effective Population ◽  
Sliding Windows ◽  
Multispecies Coalescent ◽  
A Genome ◽  
Tree Inference ◽  
Rate Of Decay ◽  
Coalescent Time

AbstractA key distinction between species tree inference under the multi-species coalescent model (MSC), and the inference of gene trees in sliding windows along a genome, is in the effect of genetic linkage. Whereas the MSC explicitly assumes genealogies to be unlinked, i.e., statistically independent, genealogies located close together on genomes are spatially auto-correlated. Here we use tree sequence simulations with recombination to explore the effects of species tree parameters on spatial patterns of linkage among genealogies. We decompose coalescent time units to demonstrate differential effects of generation time and effective population size on spatial coalescent patterns, and we define a new metric, “phylogenetic linkage,” for measuring the rate of decay of phylogenetic similarity by comparison to distances among unlinked genealogies. Finally, we provide a simple example where accounting for phylogenetic linkage in sliding window analyses improves local gene tree inference.

Comparative evolutionary genetics of trematode parasites (Plagiorchiidae) and their anuran hosts

1992 ◽  
Vol 70 (5) ◽  
pp. 993-1000 ◽  
Author(s):  
B. H. Rannala
Keyword(s):  
Genetic Distance ◽  
Protein Evolution ◽  
Molecular Clock ◽  
Sampling Error ◽  
Evolutionary Genetics ◽  
Genetic Distances ◽  
Trematode Species ◽  
Phylogenetic Hypotheses ◽  
Trematode Parasites

A study of five trematode species of the genera Glypthelmins and Haplometrana inhabiting anurans produced allozyme-based estimates of Nei's (1978) genetic distance ranging from 0.126 to 1.867. An estimate of trematode phylogeny is in agreement with earlier morphologically based phylogenetic hypotheses and is similar to the phylogeny for associated host ranid and hylid frogs based on rDNA and morphology. A comparison of the genetic distances observed among trematodes with those of their respective hosts suggests that host and parasite genetic distances are not significantly correlated. This is counter to expectations based on a molecular clock for protein evolution in hosts and parasites. These results may reflect (i) the effects of sampling error on genetic distance estimates, (ii) a non-clocklike rate of protein evolution in hosts and (or) parasites, (iii) temporally independent speciation events in associated host and parasite lineages, or (iv) the effects of host hybridization.

scholarly journals Contingency and entrenchment in protein evolution under purifying selection

2015 ◽  
Vol 112 (25) ◽  
pp. E3226-E3235 ◽  
Author(s):  
Premal Shah ◽  
David M. McCandlish ◽  
Joshua B. Plotkin
Keyword(s):  
Ligand Binding ◽  
Protein Evolution ◽  
Protein Sequence ◽  
Computational Models ◽  
Purifying Selection ◽  
Sequence Evolution ◽  
Phenotypic Effect ◽  
Protein Divergence ◽  
Protein Sequence Evolution ◽  
Over Time

The phenotypic effect of an allele at one genetic site may depend on alleles at other sites, a phenomenon known as epistasis. Epistasis can profoundly influence the process of evolution in populations and shape the patterns of protein divergence across species. Whereas epistasis between adaptive substitutions has been studied extensively, relatively little is known about epistasis under purifying selection. Here we use computational models of thermodynamic stability in a ligand-binding protein to explore the structure of epistasis in simulations of protein sequence evolution. Even though the predicted effects on stability of random mutations are almost completely additive, the mutations that fix under purifying selection are enriched for epistasis. In particular, the mutations that fix are contingent on previous substitutions: Although nearly neutral at their time of fixation, these mutations would be deleterious in the absence of preceding substitutions. Conversely, substitutions under purifying selection are subsequently entrenched by epistasis with later substitutions: They become increasingly deleterious to revert over time. Our results imply that, even under purifying selection, protein sequence evolution is often contingent on history and so it cannot be predicted by the phenotypic effects of mutations assayed in the ancestral background.

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