scholarly journals A TWO-LOCUS NEUTRALITY TEST: APPLICATIONS TO HUMANS, E. COLI AND LODGEPOLE PINE

Genetics ◽  
1986 ◽  
Vol 112 (1) ◽  
pp. 135-156
Author(s):  
Philip W Hedrick ◽  
Glenys Thomson
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Lodgepole Pine ◽  
The Other ◽  
Effective Population ◽  
Recombination Rates ◽  
Neutrality Test ◽  
E Coli ◽  
Electrophoretic Data

ABSTRACT The expected disequilibrium between two loci with k alleles at one locus and l alleles at the other is given for a sample of size n drawn from a population under neutrality equilibrium. Three different measures of disequilibrium with 95% intervals are tabulated for combinations of n, k, l and 4Nc, where N is the effective population size and c is the amount of recombination between the loci. The extent and pattern of disequilibrium are strongly dependent upon 4Nc and are somewhat dependent on n, k and l. The 95% intervals are large, particularly for low numbers of alleles and low values of 4Nc. As examples, observed disequilibrium from histocompatibility loci in humans (HLA) and electrophoretic data in E. coli and lodgepole pine were compared to these theoretical values. Using information about recombination rates, the HLA data showed more disequilibrium than neutrality expectations, whereas electrophoretic data from E. coli and lodgepole pine had somewhat less disequilibrium than neutrality expectations.

scholarly journals The population genetics of haplo-diploids and X-linked genes

1984 ◽  
Vol 44 (3) ◽  
pp. 321-341 ◽  
Author(s):  
P. J. Avery
Keyword(s):  
Population Genetics ◽  
Genetic Variability ◽  
Population Size ◽  
Effective Population Size ◽  
Disease Genes ◽  
Effective Population ◽  
Random Drift ◽  
Mutation Pressure ◽  
Electrophoretic Data ◽  
Fitness Parameters

SUMMARYFrom the available electrophoretic data, it is clear that haplodiploid insects have a much lower level of genetic variability than diploid insects, a difference that is only partially explained by the social structure of some haplodiploid species. The data comparing X-linked genes and autosomal genes in the same species is much more sparse and little can be inferred from it. This data is compared with theoretical analyses of X-linked genes and genes in haplodiploids. (The theoretical population genetics of X-linked genes and genes in haplodiploids are identical.) X-linked genes under directional selection will be lost or fixed more quickly than autosomal genes as selection acts more directly on X-linked genes and the effective population size is smaller. However, deleterious disease genes, maintained by mutation pressure, will give higher disease incidences at X-linked loci and hence rare mutants are easier to detect at X-linked loci. Considering the forces which can maintain balanced polymorphisms, there are much stronger restrictions on the fitness parameters at X-linked loci than at autosomal loci if genetic variability is to be maintained, and thus fewer polymorphic loci are to be expected on the X-chromosome and in haplodiploids. However, the mutation-random drift hypothesis also leads to the expectation of lower heterozygosity due to the decrease in effective population size. Thus the theoretical results fit in with the data but it is still subject to argument whether selection or mutation-random drift are maintaining most of the genetic variability at X-linked genes and genes in haplodiploids.

Microsatellite loci over a thirty-three year period for a malaria parasite (Plasmodium mexicanum): bottleneck in effective population size and effect on allele frequencies

Parasitology ◽  
2012 ◽  
Vol 140 (1) ◽  
pp. 21-28 ◽  
Author(s):  
J. J. SCHALL ◽  
K. M. ST. DENIS
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Malaria Parasite ◽  
Genetic Data ◽  
Parasite Prevalence ◽  
Allele Frequencies ◽  
The Other ◽  
Effective Population ◽  
Blood Smears ◽  
Parasite Plasmodium

SUMMARYChanges in population allele frequencies may be driven by several forces, including selection and drift, and are revealed only by sampling over many generations. Such studies, however, are rare for protist parasites. Microsatellite allele frequencies for 4 loci were followed in a population of Plasmodium mexicanum, a malaria parasite of lizards in California USA at 1 site from 1978 to 2010. Rapid turnover of the lizards indicates the parasite was studied for a minimum of 33 transmission cycles and possibly twice that number. Sample sizes ranged from 841 to 956 scored parasite clones per locus. DNA was extracted from frozen dried blood and blood removed from stained blood smears from the earliest years, and a verification study demonstrated DNA from the blood smears provided valid genetic data. Parasite prevalence and effective population size (Ne) dropped after 2000, remaining lower for the next decade. For 2 loci, allele frequencies appeared stable for the first 2 decades of the study, but changed more rapidly after the decline in prevalence. Allele frequencies changed more gradually for the other 2 loci. Genetic drift could account for changes in allele frequencies, especially after the drop in prevalence and Ne, but the force of selection could also have driven the observed patterns.

Development of flowering and the effect of pruning in a clonal seed orchard of lodgepole pine

1994 ◽  
Vol 24 (1) ◽  
pp. 71-76 ◽  
Author(s):  
Anders Fries
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Lodgepole Pine ◽  
Seed Orchard ◽  
Effective Population ◽  
Clonal Seed Orchard ◽  
Crown Volume ◽  
Female Flowering ◽  
Male Strobili

The development of female and male flowering among 20 clones was studied in a clonal seed orchard of lodgepole pine (Pinuscontorta var. latifolia Engelm.) in central Sweden. Flowering in relation to height, crown volume, and pruning was also studied. Twelve years after grafting (7 years after field planting), female flowering averaged 43 strobili per graft while male strobili were few. Eighteen years from grafting, the number of female and male strobuli were 143 and 142, respectively. The female effective population size was around 80% of maximum and was stable during the whole period. The male effective population size increased from 25 to 68%. Index of monoecy increased from 58 to 81% of maximum. The results indicate that at around 18 years after grafting, female and male flowering were satisfactorily distributed among the clones. There were no clonal correlations between male flowering and female flowering, while correlations between years for those traits separately were strong. Male flowering showed stronger correlation to the size of the graft than female flowering.

scholarly journals Genome-Wide Patterns of Homozygosity and Relevant Characterizations on the Population Structure in Piétrain Pigs

Genes ◽  
2020 ◽  
Vol 11 (5) ◽  
pp. 577
Author(s):  
Huiwen Zhan ◽  
Saixian Zhang ◽  
Kaili Zhang ◽  
Xia Peng ◽  
Shengsong Xie ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Population Size ◽  
Effective Population Size ◽  
Average Length ◽  
The Other ◽  
Runs Of Homozygosity ◽  
Effective Population ◽  
Inbreeding Coefficients ◽  
Genome Wide ◽  
Genomic Regions

Investigating the patterns of homozygosity, linkage disequilibrium, effective population size and inbreeding coefficients in livestock contributes to our understanding of the genetic diversity and evolutionary history. Here we used Illumina PorcineSNP50 Bead Chip to identify the runs of homozygosity (ROH) and estimate the linkage disequilibrium (LD) across the whole genome, and then predict the effective population size. In addition, we calculated the inbreeding coefficients based on ROH in 305 Piétrain pigs and compared its effect with the other two types of inbreeding coefficients obtained by different calculation methods. A total of 23,434 ROHs were detected, and the average length of ROH per individual was about 507.27 Mb. There was no regularity on how those runs of homozygosity distributed in genome. The comparisons of different categories suggested that the formation of long ROH was probably related with recent inbreeding events. Although the density of genes located in ROH core regions is lower than that in the other genomic regions, most of them are related with Piétrain commercial traits like meat qualities. Overall, the results provide insight into the way in which ROH is produced and the identified ROH core regions can be used to map the genes associated with commercial traits in domestic animals.

Estimating Ancestral Population Sizes and Divergence Times

Genetics ◽  
2003 ◽  
Vol 163 (1) ◽  
pp. 395-404 ◽  
Author(s):  
Jeffrey D Wall
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Sequence Data ◽  
Ancestral Population ◽  
Divergence Times ◽  
Intragenic Recombination ◽  
Intergenic Sequence ◽  
Effective Population ◽  
Recombination Rates ◽  
Population Sizes

Abstract This article presents a new method for jointly estimating species divergence times and ancestral population sizes. The method improves on previous ones by explicitly incorporating intragenic recombination, by utilizing orthologous sequence data from closely related species, and by using a maximum-likelihood framework. The latter allows for efficient use of the available information and provides a way of assessing how much confidence we should place in the estimates. I apply the method to recently collected intergenic sequence data from humans and the great apes. The results suggest that the human-chimpanzee ancestral population size was four to seven times larger than the current human effective population size and that the current human effective population size is slightly >10,000. These estimates are similar to previous ones, and they appear relatively insensitive to assumptions about the recombination rates or mutation rates across loci.

scholarly journals Evolution of a Dominant Natural Isolate ofEscherichia coliin the Human Gut over the Course of a Year Suggests a Neutral Evolution with Reduced Effective Population Size

2018 ◽  
Vol 84 (6) ◽  
Author(s):  
Mohamed Ghalayini ◽  
Adrien Launay ◽  
Antoine Bridier-Nahmias ◽  
Olivier Clermont ◽  
Erick Denamur ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Population Size ◽  
Effective Population Size ◽  
Experimental Evolution ◽  
Neutral Evolution ◽  
Effective Population ◽  
Human Gut ◽  
Healthy Human ◽  
Content Type ◽  
E Coli

ABSTRACTIn vitroandin vivoevolution experiments onEscherichia colirevealed several principles of bacterial adaptation. However, few data are available in the literature describing the behavior ofE. coliin its natural environment. We attempted here to study the evolution in the human gut of a commensal dominantE. coliclone, ED1a belonging to the B2 phylogroup, through a longitudinal genomic study. We sequenced 24 isolates sampled at three different time points within a healthy individual over almost a year. We computed a mutation rate of 6.90 × 10−7mutations per base per year of the chromosome forE. coliED1a in healthy human gut. We observed very limited genomic diversity and could not detect any evidence of selection, in contrast to what is observed in experimental evolution over a similar length of time. We therefore suggest that ED1a, being well adapted to the healthy human gut, evolves mostly neutrally with a low effective population size (Neof ≈500 to 1,700).IMPORTANCEIn this study, we follow the genomic fate of a dominant clone ofEscherichia coliin the human gut of a healthy individual over about a year. We could compute a low annual mutation rate that supports low diversity, and we could not retrieve any clear signature of selection. These observations support a neutral evolution ofE. coliin the human gut, compatible with a very limited effective population size that deviates drastically with the observations made previously in experimental evolution.

scholarly journals Selection Intensity for Codon Bias and the Effective Population Size of Escherichia coli

Genetics ◽  
1996 ◽  
Vol 142 (4) ◽  
pp. 1379-1382 ◽  
Author(s):  
Otto G Berg
Keyword(s):  
Escherichia Coli ◽  
Population Structure ◽  
Population Size ◽  
Effective Population Size ◽  
Codon Bias ◽  
Recent Literature ◽  
The Other ◽  
Selection Intensity ◽  
Effective Population ◽  
Synonymous Substitutions

Abstract The selection intensity for codon bias and the synonymous diversity have been used in the recent literature to estimate the effective population size of Escherichia coli. The results have varied between 105 and 108. It is suggested here that most of this disparity can be explained by a model that accounts for the population structure of the species. Thus it is assumed that weakly selected characters, like synonymous substitutions, are selectively fixed within individual lines or colonies but spread throughout the population in an essentially neutral way when colonies replace one another. In this way, the effective population size that enters expressions for the codon bias will be that of an individual colony, which, if hitchhiking effects are considered, can be a very small number. The effective population size that appears together with the mutation rate in expressions for the synonymous diversity, on the other hand, will be related to the total number of colonies that make up the species and can be a very large number.

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