scholarly journals Controlling for variable transposition rate with an age-adjusted site frequency spectrum

2021 ◽  
Author(s):  
Robert Horvath ◽  
Mitra Menon ◽  
Michelle C Stitzer ◽  
Jeffrey Ross-Ibarra
Keyword(s):  
Frequency Spectrum ◽  
Age Distribution ◽  
Empirical Work ◽  
Low Frequency ◽  
Purifying Selection ◽  
Selective Constraint ◽  
Correct Identification ◽  
Weak Selection ◽  
Transposition Rate ◽  
Site Frequency Spectrum

Recognition of the important role of transposable elements (TEs) in eukaryotic genomes quickly led to a burgeoning literature modeling and estimating the effects of selection on TEs. Much of the empirical work on selection has focused on analyzing the site frequency spectrum (SFS) of TEs. But TEs differ from standard evolutionary models in a number of ways that can impact the power and interpretation of the SFS. For example, rather than mutating under a clock-like model, transposition often occurs in bursts which can inflate particular frequency categories compared to expectations under a standard neutral model. If a TE burst has been recent, the excess of low frequency polymorphisms can mimic the effect of purifying selection. Here, we investigate how transposition bursts affect the frequency distribution of TEs and the correlation between age and allele frequency. Using information on the TE age distribution, we propose an age-adjusted site frequency spectrum to compare TEs and neutral polymorphisms to more effectively evaluate whether TEs are under selective constraints. We show that our approach can minimize instances of false inference of selective constraint, but also allows for a correct identification of even weak selection affecting TEs which experienced a transposition burst and is robust to at least simple demographic changes. The results presented here will help researchers working on TEs to more reliably identify the effects of selection on TEs without having to rely on the assumption of a constant transposition rate.

scholarly journals The effect of strong purifying selection on genetic diversity

2017 ◽  
Author(s):  
Ivana Cvijović ◽  
Benjamin H. Good ◽  
Michael M. Desai
Keyword(s):  
Genetic Diversity ◽  
Frequency Spectrum ◽  
Purifying Selection ◽  
Genomic Diversity ◽  
Small Samples ◽  
Direct Selection ◽  
Background Selection ◽  
Deleterious Mutations ◽  
Site Frequency Spectrum ◽  
Neutral Mutations

Purifying selection reduces genetic diversity, both at sites under direct selection and at linked neutral sites. This process, known as background selection, is thought to play an important role in shaping genomic diversity in natural populations. Yet despite its importance, the effects of background selection are not fully understood. Previous theoretical analyses of this process have taken a backwards-time approach based on the structured coalescent. While they provide some insight, these methods are either limited to very small samples or are computationally prohibitive. Here, we present a new forward-time analysis of the trajectories of both neutral and deleterious mutations at a nonrecombining locus. We find that strong purifying selection leads to remarkably rich dynamics: neutral mutations can exhibit sweep-like behavior, and deleterious mutations can reach substantial frequencies even when they are guaranteed to eventually go extinct. Our analysis of these dynamics allows us to calculate analytical expressions for the full site frequency spectrum. We find that whenever background selection is strong enough to lead to a reduction in genetic diversity, it also results in substantial distortions to the site frequency spectrum, which can mimic the effects of population expansions or positive selection. Because these distortions are most pronounced in the low and high frequency ends of the spectrum, they become particularly important in larger samples, but may have small effects in smaller samples. We also apply our forward-time framework to calculate other quantities, such as the ultimate fates of polymorphisms or the fitnesses of their ancestral backgrounds.

Preferential acceleration of heavy ions from thermal velocities

1968 ◽  
Vol 46 (10) ◽  
pp. S638-S641 ◽  
Author(s):  
D. B. Melrose
Keyword(s):  
Frequency Spectrum ◽  
High Frequency ◽  
Heavy Ions ◽  
Crab Nebula ◽  
Low Frequency ◽  
High Frequency Waves ◽  
Hydromagnetic Waves ◽  
The Crab Nebula ◽  
Low Frequency Waves

The acceleration of ions from thermal velocities is analyzed to determine conditions under which heavy ions can be preferentially accelerated. Two accelerating mechanisms involving high-and low-frequency hydromagnetic waves respectively are considered. Preferential acceleration of heavy ions occurs for high-frequency waves if the frequency spectrum falls off faster than (frequency)−1. For the low-frequency waves heavy ions are less effectively accelerated than lighter ions. However, very heavy ions can be preferentially accelerated, the abundances of the very heavy ions being enhanced by a factor Ai over the thermal abundances. Acceleration of ions in the envelope of the Crab nebula is considered as an example.

Revision of the estimates of glutenin gene effects at the Glu-B1 locus from southern Australian wheat breeding programs

2004 ◽  
Vol 55 (10) ◽  
pp. 1093 ◽  
Author(s):  
H. A. Eagles ◽  
R. F. Eastwood ◽  
G. J. Hollamby ◽  
E. M. Martin ◽  
G. B. Cornish
Keyword(s):  
Development Time ◽  
Low Frequency ◽  
Wheat Breeding ◽  
Correct Identification ◽  
Gene Effects ◽  
Breeding Programs ◽  
Multiple Alleles ◽  
Intermediate Allele ◽  
Dough Extensibility ◽  
Dough Development Time

Glutenins are the major determinant of dough characteristics in wheat. These proteins are determined by genes at 6 loci, with multiple alleles present in southern Australian breeding programs. Previously, we estimated the effects of these genes on maximum dough resistance (Rmax), dough extensibility and dough development time. Subsequently, the allele previously classified as Glu-B1b was found to consist of 2 alleles, with one, now considered to be Glu-B1al, producing an overexpression of the Bx7 glutenin subunit. Therefore, there is a potential bias in our previous estimates. An extended dataset was analysed with the 2 alleles now separated. These analyses identified negligible biases in our previous estimates, probably due to a low frequency of Glu-B1al before 1999. However, Glu-B1al produced significantly higher Rmax, dough extensibility, and dough development time values than all other alleles at the Glu-B1 locus. Therefore, at intermediate allele frequencies, substantial bias in estimates of the effects of the Glu-B1 alleles can be expected without correct identification of Glu-B1al.

scholarly journals Diversity of and Selection Acting on CylindrospermopsincyrBGene Adenylation Domain Sequences in Florida

2011 ◽  
Vol 77 (7) ◽  
pp. 2502-2507 ◽  
Author(s):  
Mete Yilmaz ◽  
Edward J. Phlips
Keyword(s):  
United States ◽  
Low Frequency ◽  
Purifying Selection ◽  
The United States ◽  
The Other ◽  
Cylindrospermopsis Raciborskii ◽  
Adenylation Domain ◽  
Other Hand ◽  
Neutrality Tests ◽  
The One

ABSTRACTAphanizomenon ovalisporumis the only confirmed cylindrospermopsin producer identified in the United States to date. On the other hand,Cylindrospermopsis raciborskiiis a prominent feature of many lakes in Florida and other regions of the United States. To see the variation in cylindrospermopsincyrBgene adenylation domain sequences and possibly discover new cylindrospermopsin producers, we collected water samples for a 3-year period from 17 different systems in Florida. Positive amplicons were cloned and sequenced, revealing that approximately 92% of sequences wereA. ovalisporum-like (>99% identity). Interestingly, 6% of sequences were very similar (>99% identity) tocyrBsequences ofC. raciborskiifrom Australia and ofAphanizomenonsp. from Germany. Neutrality tests suggest thatA. ovalisporum-likecyrBadenylation domain sequences are under purifying selection, with abundant low-frequency polymorphisms within the population. On the other hand, when compared between species by codon-based methods, amino acids of CyrB also seem to be under purifying selection, in accordance with the one proposed amino acid thought to be activated by the CyrB adenylation domain.

scholarly journals Non-parametric estimation of population size changes from the site frequency spectrum

2017 ◽  
Author(s):  
Berit Lindum Waltoft ◽  
Asger Hobolth
Keyword(s):  
Population Size ◽  
Frequency Spectrum ◽  
Goodness Of Fit ◽  
Weighted Average ◽  
Cubic Spline ◽  
Parametric Estimation ◽  
New Method ◽  
Eigenvalue Decomposition ◽  
Human Populations ◽  
Site Frequency Spectrum

AbstractThe variability in population size is a key quantity for understanding the evolutionary history of a species. We present a new method, CubSFS, for estimating the changes in population size of a panmictic population from the site frequency spectrum. First, we provide a straightforward proof for the expression of the expected site frequency spectrum depending only on the population size. Our derivation is based on an eigenvalue decomposition of the instantaneous coalescent rate matrix. Second, we solve the inverse problem of determining the variability in population size from an observed SFS. Our solution is based on a cubic spline for the population size. The cubic spline is determined by minimizing the weighted average of two terms, namely (i) the goodness of fit to the SFS, and (ii) a penalty term based on the smoothness of the changes. The weight is determined by cross-validation. The new method is validated on simulated demographic histories and applied on data from nine different human populations.

scholarly journals The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: the effects of sequencing techniques and sampling strategies

2018 ◽  
Author(s):  
Christelle Fraïsse ◽  
Camille Roux ◽  
Pierre-Alexandre Gagnaire ◽  
Jonathan Romiguier ◽  
Nicolas Faivre ◽  
...  
Keyword(s):  
Frequency Spectrum ◽  
Approximate Bayesian Computation ◽  
Exome Capture ◽  
Bayesian Computation ◽  
Sampling Strategies ◽  
Migration Rates ◽  
History Of ◽  
Site Frequency Spectrum ◽  
Approximate Bayesian ◽  
Number Of Individuals

AbstractGenome-scale diversity data are increasingly available in a variety of biological systems, and can be used to reconstruct the past evolutionary history of species divergence. However, extracting the full demographic information from these data is not trivial, and requires inferential methods that account for the diversity of coalescent histories throughout the genome. Here, we evaluate the potential and limitations of one such approach. We reexamine a well-known system of mussel sister species, using the joint site frequency spectrum (jSFS) of synonymous mutations computed either from exome capture or RNA-seq, in an Approximate Bayesian Computation (ABC) framework. We first assess the best sampling strategy (number of: individuals, loci, and bins in the jSFS), and show that model selection is robust to variation in the number of individuals and loci. In contrast, different binning choices when summarizing the joint site frequency spectrum, strongly affect the results: including classes of low and high frequency shared polymorphisms can more effectively reveal recent migration events. We then take advantage of the flexibility of ABC to compare more realistic models of speciation, including variation in migration rates through time (i.e. periodic connectivity) and across genes (i.e. genome-wide heterogeneity in migration rates). We show that these models were consistently selected as the most probable, suggesting that mussels have experienced a complex history of gene flow during divergence and that the species boundary is semi-permeable. Our work provides a comprehensive evaluation of ABC demographic inference in mussels based on the coding site frequency spectrum, and supplies guidelines for employing different sequencing techniques and sampling strategies. We emphasize, perhaps surprisingly, that inferences are less limited by the volume of data, than by the way in which they are analyzed.

scholarly journals Impacts of Diabetes, Aging, and Hearing Loss on Speech-on-Speech Masking and Spatial Release in a Large Veteran Cohort

2021 ◽  
pp. 1-14
Author(s):  
Sarah M. Theodoroff ◽  
Frederick J. Gallun ◽  
Garnett P. McMillan ◽  
Michelle Molis ◽  
Nirmal Srinivasan ◽  
...  
Keyword(s):  
Hearing Loss ◽  
Pure Tone ◽  
Mixed Model ◽  
Linear Mixed Model ◽  
Low Frequency ◽  
Correct Identification ◽  
Speech Understanding ◽  
Impaired Hearing ◽  
Pure Tone Average ◽  
Spatial Release

Purpose Type 2 diabetes mellitus (DM2) is associated with impaired hearing. However, the evidence is less clear if DM2 can lead to difficulty understanding speech in complex acoustic environments, independently of age and hearing loss effects. The purpose of this study was to estimate the magnitude of DM2-related effects on speech understanding in the presence of competing speech after adjusting for age and hearing. Method A cross-sectional study design was used to investigate the relationship between DM2 and speech understanding in 190 Veterans ( M age = 47 years, range: 25–76). Participants were classified as having no diabetes ( n = 74), prediabetes ( n = 19), or DM2 that was well controlled ( n = 24) or poorly controlled ( n = 73). A test of spatial release from masking (SRM) was presented in a virtual acoustical simulation over insert earphones with multiple talkers using sentences from the coordinate response measure corpus to determine the target-to-masker ratio (TMR) required for 50% correct identification of target speech. A linear mixed model of the TMR results was used to estimate SRM and separate effects of diabetes group, age, and low-frequency pure-tone average (PTA-low) and high-frequency pure-tone average. A separate model estimated the effects of DM2 on PTA-low. Results After adjusting for hearing and age, diabetes-related effects remained among those whose DM2 was well controlled, showing an SRM loss of approximately 0.5 dB. Results also showed effects of hearing loss and age, consistent with the literature on people without DM2. Low-frequency hearing loss was greater among those with DM2. Conclusions In a large cohort of Veterans, low-frequency hearing loss and older age negatively impact speech understanding. Compared with nondiabetics, individuals with controlled DM2 have additional auditory deficits beyond those associated with hearing loss or aging. These results provide a potential explanation for why individuals who have diabetes and/or are older often report difficulty understanding speech in real-world listening environments. Supplemental Material https://doi.org/10.23641/asha.16746475

scholarly journals Inferring the frequency spectrum of derived variants to quantify adaptive molecular evolution in protein-coding genes of Drosophila melanogaster

2016 ◽  
Author(s):  
Peter D. Keightley ◽  
Jose Campos ◽  
Tom Booker ◽  
Brian Charlesworth
Keyword(s):  
Amino Acid ◽  
Molecular Evolution ◽  
Frequency Spectrum ◽  
Population Genomics ◽  
Selective Constraint ◽  
Accurate Estimation ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Adaptive Molecular Evolution ◽  
Amino Acid Mutations

Many approaches for inferring adaptive molecular evolution analyze the unfolded site frequency spectrum (SFS), a vector of counts of sites with different numbers of copies of derived alleles in a sample of alleles from a population. Accurate inference of the high copy number elements of the SFS is difficult, however, because of misassignment of alleles as derived versus ancestral. This is a known problem with parsimony using outgroup species. Here, we show that the problem is particularly serious if there is variation in the substitution rate among sites brought about by variation in selective constraint levels. We present a new method for inferring the SFS using one or two outgroups, which attempts to overcome the problem of misassignment. We show that two outgroups are required for accurate estimation of the SFS if there is substantial variation in selective constraints, which is expected to be the case for nonsynonymous sites of protein-coding genes. We apply the method to estimate unfolded SFSs for synonymous and nonsynonymous sites from Phase 2 of the Drosophila Population Genomics Project. We use the unfolded spectra to estimate the frequency and strength of advantageous and deleterious mutations, and estimate that ~50% of amino acid substitutions are positively selected, but that less than 0.5% of new amino acid mutations are beneficial, with a scaled selection strength of Nes ≈ 12.

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