scholarly journals Low nucleotide diversity in man.

Genetics ◽  
1991 ◽  
Vol 129 (2) ◽  
pp. 513-523 ◽  
Author(s):  
W H Li ◽  
L A Sadler
Keyword(s):  
Amino Acid ◽  
Genetic Variability ◽  
Nucleotide Diversity ◽  
Untranslated Regions ◽  
Effective Population ◽  
Base Pairs ◽  
Coding Regions ◽  
Low Diversity ◽  
Order Of Magnitude

Abstract The nucleotide diversity (pi) in humans is studied by using published cDNA and genomic sequences that have been carefully checked for sequencing accuracy. This measure of genetic variability is defined as the number of nucleotide differences per site between two randomly chosen sequences from a population. A total of more than 75,000 base pairs from 49 loci are compared. The DNA regions studied are the 5' and 3' untranslated regions and the amino acid coding regions. The coding regions are divided into nondegenerate sites (i.e., sites at which all possible changes are nonsynonymous), twofold degenerate sites (i.e., sites at each of which one of the three possible changes is synonymous) and fourfold degenerate sites (i.e., sites at which all three possible changes are synonymous). The pi values estimated are, respectively, 0.03 and 0.04% for the 5' and 3' UT regions, and 0.03, 0.06 and 0.11% for nondegenerate, twofold degenerate and fourfold degenerate sites. Since the highest pi value is only 0.11%, which is about one order of magnitude lower than those in Drosophila populations, the nucleotide diversity in humans is very low. The low diversity is probably due to a relatively small long-term effective population size rather than any severe bottleneck during human evolution.

scholarly journals A Novel Distinct Genetic Variant of Tomato Torrado Virus with Substantially Shorter RNA1-Specific 3’untranslated Region (3’UTR)

Plants ◽  
2021 ◽  
Vol 10 (11) ◽  
pp. 2454
Author(s):  
Marta Budziszewska ◽  
Przemysław Wieczorek
Keyword(s):  
Amino Acid ◽  
Genetic Variability ◽  
Untranslated Region ◽  
Genetic Variant ◽  
Sequencing Data ◽  
Sequence Analyses ◽  
Nucleotide Substitutions ◽  
Systemic Necrosis ◽  
Single Nucleotide

Tomato torrado virus (ToTV) induces severe systemic necrosis in Solanum lycopersicum. This work aimed at describing the genetic variability of necrosis-inducing ToTV-Wal’17 collected in 2017, derived from the ToTV-Wal’03 after long-term passages in plants. Sequence analyses of the ToTV-Wal’17 indicated twenty-eight single nucleotide substitutions in coding sequence of both RNAs, twelve of which resulted in amino acid changes in viral polyproteins. Moreover the sequencing data revealed that the 3’UTR of ToTV-Wal’17 RNA1 was 394 nts shorter in comparison to Wal’03. The performed sequence analyses revealed that 3’UTR of RNA1 of ToTV-Wal’17 is the most divergent across all previously described European isolates.

Chloroplast DNA phylogeography in long-lived Huon pine, a Tasmanian rain forest conifer

2008 ◽  
Vol 38 (6) ◽  
pp. 1576-1589 ◽  
Author(s):  
Catherine M. Clark ◽  
Ignazio Carbone
Keyword(s):  
Nucleotide Diversity ◽  
Isolation By Distance ◽  
Population Bottlenecks ◽  
Base Pairs ◽  
Distance Model ◽  
History Of ◽  
Lagarostrobos Franklinii ◽  
Tasmanian Endemic ◽  
Western Portion

Genealogy based methods were used to estimate phylogeographic history for a Tasmanian endemic conifer, Huon pine ( Lagarostrobos franklinii (Hook. f.) Quinn). DNA from trees in eight populations was sequenced using three chloroplast primers (trnS–trnT, trnD–trnT, and psbC–trnS). Mean nucleotide diversity was low (π = 0.000 93 ± 0.000 06) from 892 base pairs of sequence, but varied in stands from 0.0 to 0.001 15. Two of the five haplotypes were widely distributed, but the most frequently occurring haplotype was found only in the western portion of the range. Population structure was highly significant among populations overall (GST = 0.261, where GST is the coefficient of gene differentiation, and p ≤ 0.0001), and there were indications of significant isolation by distance (p ≤ 0.022). Populations exhibited the highest levels of differentiation between the southeastern and northwestern watersheds. Estimates of migration between populations obtained using both parametric and nonparametric methods indicated levels of gene flow consistent with an isolation by distance model. Nested clade analysis demonstrated a pattern of genetic diversity in Huon pine that is consistent with a history of range expansion. The exceptionally low level of nucleotide diversity, haplotype distribution, and paleoecological data are congruent with a history of long-term range reduction, population bottlenecks, and subsequent colonization events from refugial areas.

scholarly journals Genetic variability in cysteine protease genes ofHaemonchus contortus

Parasitology ◽  
2004 ◽  
Vol 128 (5) ◽  
pp. 549-559 ◽  
Author(s):  
A. RUIZ ◽  
J. M. MOLINA ◽  
A. NJUE ◽  
R. K. PRICHARD
Keyword(s):  
Amino Acid ◽  
Nucleotide Sequence ◽  
Genetic Variability ◽  
Amino Acid Sequence ◽  
Cysteine Protease ◽  
Haemonchus Contortus ◽  
Significant Variation ◽  
Nucleotide Diversity ◽  
Cysteine Proteases ◽  
Different Strains

To increase the existent genetic variability in cysteine proteases, a polymorphism study was performed inHaemonchus contortusby comparing 2 different strains of the parasite: North American (NA) and Spanish (SP) strains. For this purpose, the polymorphism of 5 previously reported genes (AC-1,AC-3,AC-4,AC-5andGCP-7) were analysed by PCR–SSCP and sequencing procedures. Based on the SSCP results, a total of 20 different alleles were identified for the 5lociassessed. Exceptlocus AC-5, all thelociwere polymorphic.Loci AC-1,AC-3,AC-4andGCP-7showed 5, 8, 2 and 4 alleles, respectively. The allelic frequencies ranged from 0·0070 to 0·8560 and were significantly different between strains. In addition, nucleotide diversity analyses showed a significant variation within and between strains. The variations in the nucleotide sequence of the different alleles were translated in some cases into changes in the amino acid sequence. Evidence of genetic variability in cysteine proteases from two different strains ofH. contortusfor the same set of genes had not been previously reported.

scholarly journals How much does Ne vary among species?

2019 ◽  
Author(s):  
Nicolas Galtier ◽  
Marjolaine Rousselle
Keyword(s):  
Amino Acid ◽  
Population Genomics ◽  
Species Variation ◽  
Effective Population ◽  
Gamma Model ◽  
Frequency Spectra ◽  
Synonymous Mutations ◽  
Evolutionary Force ◽  
Order Of Magnitude ◽  
The Impact

AbstractGenetic drift is an important evolutionary force of strength inversely proportional to Ne, the effective population size. The impact of drift on genome diversity and evolution is known to vary among species, but quantifying this effect is a difficult task. Here we assess the magnitude of variation in drift power among species of animals via its effect on the mutation load – which implies also inferring the distribution of fitness effects of deleterious mutations (DFE). To this aim, we analyze the non-synonymous (amino-acid changing) and synonymous (amino-acid conservative) allele frequency spectra in a large sample of metazoan species, with a focus on the primates vs. fruit flies contrast. We show that a Gamma model of the DFE is not suitable due to strong differences in estimated shape parameters among taxa, while adding a class of lethal mutations essentially solves the problem. Using the Gamma + lethal model and assuming that the mean deleterious effects of non-synonymous mutations is shared among species, we estimate that the power of drift varies by a factor of at least 500 between large-Ne and small-Ne species of animals, i.e., an order of magnitude more than the among-species variation in genetic diversity. Our results are relevant to Lewontin’s paradox while further questioning the meaning of the Ne parameter in population genomics.

scholarly journals Determinants of the Efficacy of Natural Selection on Coding and Noncoding Variability in Two Passerine Species

2017 ◽  
Vol 9 (11) ◽  
pp. 2987-3007 ◽  
Author(s):  
Pádraic Corcoran ◽  
Toni I Gossmann ◽  
Henry J Barton ◽  
Jon Slate ◽  
Kai Zeng ◽  
...  
Keyword(s):  
Zebra Finch ◽  
Recombination Rate ◽  
Nucleotide Diversity ◽  
Purifying Selection ◽  
Great Tit ◽  
Untranslated Regions ◽  
Demographic Model ◽  
Zebra Finches ◽  
Effective Population ◽  
Biased Gene Conversion

Abstract Population genetic theory predicts that selection should be more effective when the effective population size (Ne) is larger, and that the efficacy of selection should correlate positively with recombination rate. Here, we analyzed the genomes of ten great tits and ten zebra finches. Nucleotide diversity at 4-fold degenerate sites indicates that zebra finches have a 2.83-fold larger Ne. We obtained clear evidence that purifying selection is more effective in zebra finches. The proportion of substitutions at 0-fold degenerate sites fixed by positive selection (α) is high in both species (great tit 48%; zebra finch 64%) and is significantly higher in zebra finches. When α was estimated on GC-conservative changes (i.e., between A and T and between G and C), the estimates reduced in both species (great tit 22%; zebra finch 53%). A theoretical model presented herein suggests that failing to control for the effects of GC-biased gene conversion (gBGC) is potentially a contributor to the overestimation of α, and that this effect cannot be alleviated by first fitting a demographic model to neutral variants. We present the first estimates in birds for α in the untranslated regions, and found evidence for substantial adaptive changes. Finally, although purifying selection is stronger in high-recombination regions, we obtained mixed evidence for α increasing with recombination rate, especially after accounting for gBGC. These results highlight that it is important to consider the potential confounding effects of gBGC when quantifying selection and that our understanding of what determines the efficacy of selection is incomplete.

scholarly journals How Much Does Ne Vary Among Species?

Genetics ◽  
2020 ◽  
Vol 216 (2) ◽  
pp. 559-572 ◽  
Author(s):  
Nicolas Galtier ◽  
Marjolaine Rousselle
Keyword(s):  
Amino Acid ◽  
Population Genomics ◽  
Species Variation ◽  
Effective Population ◽  
Gamma Model ◽  
Frequency Spectra ◽  
Fitness Effects ◽  
Evolutionary Force ◽  
Order Of Magnitude ◽  
The Impact

Genetic drift is an important evolutionary force of strength inversely proportional to Ne, the effective population size. The impact of drift on genome diversity and evolution is known to vary among species, but quantifying this effect is a difficult task. Here we assess the magnitude of variation in drift power among species of animals via its effect on the mutation load – which implies also inferring the distribution of fitness effects of deleterious mutations. To this aim, we analyze the nonsynonymous (amino-acid changing) and synonymous (amino-acid conservative) allele frequency spectra in a large sample of metazoan species, with a focus on the primates vs. fruit flies contrast. We show that a Gamma model of the distribution of fitness effects is not suitable due to strong differences in estimated shape parameters among taxa, while adding a class of lethal mutations essentially solves the problem. Using the Gamma + lethal model and assuming that the mean deleterious effects of nonsynonymous mutations is shared among species, we estimate that the power of drift varies by a factor of at least 500 between large-Ne and small-Ne species of animals, i.e., an order of magnitude more than the among-species variation in genetic diversity. Our results are relevant to Lewontin’s paradox while further questioning the meaning of the Ne parameter in population genomics.

scholarly journals Breeding Strategies to Optimize Effective Population Size in Low Census Captive Populations: The Case of Gazella cuvieri

Animals ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 1559
Author(s):  
Candela Ojeda-Marín ◽  
Isabel Cervantes ◽  
Eulalia Moreno ◽  
Félix Goyache ◽  
Juan Pablo Gutiérrez
Keyword(s):  
Genetic Variability ◽  
Population Size ◽  
Effective Population Size ◽  
Significant Loss ◽  
Breeding Systems ◽  
Effective Population ◽  
Evolutionary Pattern ◽  
Animal Populations ◽  
Captive Populations

Small-sized animal populations can undergo significant loss of genetic variability that can lead to their extinction. Therefore, studies on animal breeding have focused on mating systems for minimizing the disappearance of genetic variability. The main objective of this study was to compare, using computer simulations, the performance of different breeding schemes to limit the loss of genetic diversity in small-sized populations. This objective was achieved by monitoring the evolution of the effective population size obtained by 23 strategies throughout 20 generations in two populations of Gazella cuvieri. The scenarios were designed with different assumptions, in both reference subpopulations, regarding: the use of parents coancestry or offspring coancestry, the use of their increases or the coefficients themselves, and the number of males and females involved. Computations were performed using an experimental module of Endog v4.9 developed for this purpose. The results of the study showed that strategies for minimizing the coancestry of the parents were better in the short term; however, these strategies were worse in the long term. Minimizing the average coancestry of the offspring was a better approach in the long term. Nevertheless, in both populations, the best results were obtained when both the coancestry of the parents and the coancestry of the offspring were weighted at 5% each and neither males nor females were assumed to contribute to the next generation. In any case, not all strategies had the same evolutionary pattern throughout generations in both populations. The current results show that neither traditional nor new strategies have any general use. Therefore, it is important to carefully test these strategies before applying them to different populations with different breeding needs under different conditions, such as different generation intervals, and different natural breeding systems such as monogamy or polygyny.

scholarly journals The effective population size modulates the strength of GC biased gene conversion in two passerines

2021 ◽  
Author(s):  
Henry J Barton ◽  
Kai Zeng
Keyword(s):  
Population Size ◽  
Gene Conversion ◽  
Effective Population Size ◽  
Zebra Finch ◽  
Nucleotide Diversity ◽  
Gc Content ◽  
Effective Population ◽  
Coding Regions ◽  
Crossover Rate ◽  
Biased Gene Conversion

Understanding the determinants of genomic base composition is fundamental to understanding genome evolution. GC biased gene conversion (gBGC) is a key driving force behind genomic GC content, through the preferential incorporation of GC alleles over AT alleles during recombination, driving them towards fixation. The majority of work on gBGC has focussed on its role in coding regions, largely to address how it confounds estimates of selection. Non-coding regions have received less attention, particularly in regard to the interaction of gBGC and the effective population size (Ne) within and between species. To address this, we investigate how the strength of gBGC (B = 4Neb, where b is the conversion bias) varies within the non-coding genome of two wild passerines. We use a dataset of published high coverage genomes (10 great tits and 10 zebra finches) to estimate B, nucleotide diversity, changes in Ne, and crossover rates from linkage maps, in 1Mb homologous windows in each species. We demonstrate remarkable conservation of both B and crossover rate between species. We show that the mean strength of gBGC in the zebra finch is more than double that in the great tit, consistent with its twofold greater effective population size. B also correlates with both crossover rate and nucleotide diversity in each species. Finally, we estimate equilibrium GC content from both divergence and polymorphism data, which indicates that B has been increasing in both species, and provide support for population expansion explaining a large proportion of this increase in the zebra finch.

Comparison of the Potency of 8-L-Arginine, 8-D-Arginine and 8-D-Homoarginine Vasopressin Analogs with Substituted Phenylalanine in Position 2

1994 ◽  
Vol 59 (6) ◽  
pp. 1439-1450 ◽  
Author(s):  
Miroslava Žertová ◽  
Jiřina Slaninová ◽  
Zdenko Procházka
Keyword(s):  
Amino Acid ◽  
Solid Phase Synthesis ◽  
Solid Phase ◽  
Basic Amino Acid ◽  
The Other ◽  
Side Chain ◽  
Inhibitory Potency ◽  
Phase Synthesis ◽  
Other Hand ◽  
Order Of Magnitude

An analysis of the uterotonic potencies of all analogs having substituted L- or D-tyrosine or -phenylalanine in position 2 and L-arginine, D-arginine or D-homoarginine in position 8 was made. The series of analogs already published was completed by the solid phase synthesis of ten new analogs having L- or D-Phe, L- or D-Phe(2-Et), L- or D-Phe(2,4,6-triMe) or D-Tyr(Me) in position 2 and either L- or D-arginine in position 8. All newly synthesized analogs were found to be uterotonic inhibitors. Deamination increases both the agonistic and antagonistic potency. In the case of phenylalanine analogs the change of configuration from L to D in position 2 enhances the uterotonic inhibition for more than 1 order of magnitude. The L to D change in position 8 enhances the inhibitory potency negligibly. Prolongation of the side chain of the D-basic amino acid in position 8 seems to decrease slightly the inhibitory potency if there is L-substituted amino acid in position 2. On the other hand there is a tendency to the increase of the inhibitory potency if there is D-substituted amino acid in position 2.

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