scholarly journals Author Correction: Stairway Plot 2: demographic history inference with folded SNP frequency spectra

2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Xiaoming Liu ◽  
Yun-Xin Fu
Keyword(s):  
Demographic History ◽  
Frequency Spectra

An amendment to this paper has been published and can be accessed via the original article.

scholarly journals Blockwise Site Frequency Spectra for Inferring Complex Population Histories and Recombination

2016 ◽  
Author(s):  
Champak R. Beeravolu ◽  
Michael J. Hickerson ◽  
Laurent A.F. Frantz ◽  
Konrad Lohse
Keyword(s):  
Demographic History ◽  
Composite Likelihood ◽  
Model Organisms ◽  
Secondary Contact ◽  
Parameter Estimates ◽  
Genome Sequences ◽  
Frequency Spectra ◽  
Genome Wide ◽  
Complex Population ◽  
History Of

AbstractWe introduce ABLE (Approximate Blockwise Likelihood Estimation), a novel composite likelihood framework based on a recently introduced summary of sequence variation: the blockwise site frequency spectrum (bSFS). This simulation-based framework uses the the frequencies of bSFS configurations to jointly model demographic history and recombination and is explicitly designed to make inference using multiple whole genomes or genome-wide multi-locus data (e.g. RADSeq) catering to the needs of researchers studying model or non-model organisms respectively. The flexible nature of our method further allows for arbitrarily complex population histories using unphased and unpolarized whole genome sequences. In silico experiments demonstrate accurate parameter estimates across a range of divergence models with increasing complexity, and as a proof of principle, we infer the demographic history of the two species of orangutan from multiple genome sequences (over 160 Mbp in length) from each species. Our results indicate that the two orangutan species split approximately 650-950 thousand years ago but experienced a pulse of secondary contact much more recently, most likely during a period of low sea-level South East Asia (∼300,000 years ago). Unlike previous analyses we can reject a history of continuous gene flow and co-estimate genome-wide recombination. ABLE is available for download at https://github.com/champost/ABLE.

scholarly journals Dynamic sampling bias and overdispersion induced by skewed offspring distributions

2021 ◽  
Author(s):  
Takashi Okada ◽  
Oskar Hallatschek
Keyword(s):  
Allele Frequency ◽  
Statistical Tests ◽  
Demographic History ◽  
Natural Populations ◽  
Sampling Bias ◽  
Coarse Grained ◽  
Frequency Spectra ◽  
Scaling Hypothesis ◽  
Frequency Fluctuations ◽  
Dynamic Sampling

Natural populations often show enhanced genetic drift consistent with a strong skew in their offspring number distribution. The skew arises because the variability of family sizes is either inherently strong or amplified by population expansions, leading to so-called ‘jackpot’ events. The resulting allele frequency fluctuations are large and, therefore, challenge standard models of population genetics, which assume sufficiently narrow offspring distributions. While the neutral dynamics backward in time can be readily analyzed using coalescent approaches, we still know little about the effect of broad offspring distributions on the dynamics forward in time, especially with selection. Here, we employ an exact asymptotic analysis combined with a scaling hypothesis to demonstrate that over-dispersed frequency trajectories emerge from the competition of conventional forces, such as selection or mutations, with an emerging time-dependent sampling bias against the minor allele. The sampling bias arises from the characteristic time-dependence of the largest sampled family size within each allelic type. Using this insight, we establish simple scaling relations for allele frequency fluctuations, fixation probabilities, extinction times, and the site frequency spectra that arise when offspring numbers are distributed according to a power law n−(1+α). To demonstrate that this coarse-grained model captures a wide variety of non-equilibrium dynamics, we validate our results in traveling waves, where the phenomenon of ‘gene surfing’ can produce any exponent 1 < α < 2. We argue that the concept of a dynamic sampling bias is useful generally to develop both intuition and statistical tests for the unusual dynamics of populations with skewed offspring distributions, which can confound commonly used tests for selection or demographic history.

scholarly journals Examination of signatures of recent positive selection on genes involved in human sialic acid biology

2017 ◽  
Author(s):  
Jiyun M. Moon ◽  
David M. Aronoff ◽  
John A. Capra ◽  
Patrick Abbot ◽  
Antonis Rokas
Keyword(s):  
Sialic Acid ◽  
Positive Selection ◽  
Transfer Functions ◽  
Demographic History ◽  
Neutral Evolution ◽  
Human Lineage ◽  
Selective Sweeps ◽  
Frequency Spectra ◽  
Recent Positive Selection ◽  
Soft Selective Sweeps

AbstractSialic acids are nine carbon sugars ubiquitously found on the surfaces of vertebrate cells and are involved in various immune response-related processes. In humans, at least 58 genes spanning diverse functions, from biosynthesis and activation to recycling and degradation, are involved in sialic acid biology. Because of their role in immunity, sialic acid biology genes have been hypothesized to exhibit elevated rates of evolutionary change. Consistent with this hypothesis, several genes involved in sialic acid biology have experienced higher rates of non-synonymous substitutions in the human lineage than their counterparts in other great apes, perhaps in response to ancient pathogens that infected hominins millions of years ago (paleopathogens). To test whether sialic acid biology genes have also experienced more recent positive selection during the evolution of the modern human lineage, reflecting adaptation to contemporary cosmopolitan or geographically-restricted pathogens, we examined whether their protein-coding regions showed evidence of recent hard and soft selective sweeps. This examination involved the calculation of four measures that quantify changes in allele frequency spectra, extent of population differentiation, and haplotype homozygosity caused by recent hard and soft selective sweeps for 55 sialic acid biology genes using publicly available whole genome sequencing data from 1,668 humans from three ethnic groups. To disentangle evidence for selection from confounding demographic effects, we compared the observed patterns in sialic acid biology genes to simulated sequences of the same length under a model of neutral evolution that takes into account human demographic history. We found that the patterns of genetic variation of most sialic acid biology genes did not significantly deviate from neutral expectations and were not significantly different among genes belonging to different functional categories. Those few sialic acid biology genes that significantly deviated from neutrality either experienced soft sweeps or population-specific hard sweeps. Interestingly, while most hard sweeps occurred on genes involved in sialic acid recognition, most soft sweeps involved genes associated with recycling, degradation and activation, transport, and transfer functions. We propose that the lack of signatures of recent positive selection for the majority of the sialic acid biology genes is consistent with the view that these genes regulate immune responses against ancient rather than contemporary cosmopolitan or geographically restricted pathogens.

scholarly journals Stairway Plot 2: demographic history inference with folded SNP frequency spectra

2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Xiaoming Liu ◽  
Yun-Xin Fu
Keyword(s):  
Demographic History ◽  
Genotyping By Sequencing ◽  
Program Package ◽  
Nonparametric Method ◽  
Conservation Genomics ◽  
Frequency Spectra ◽  
Sequencing Technologies ◽  
Cross Platform

AbstractInferring the demographic histories of populations has wide applications in population, ecological, and conservation genomics. We present Stairway Plot 2, a cross-platform program package for this task using SNP frequency spectra. It is based on a nonparametric method with the capability of handling folded SNP frequency spectra (that is, when the ancestral alleles of the SNPs are unknown) of thousands of samples produced with genotyping-by-sequencing technologies; therefore, it is particularly suitable for nonmodel organisms.

scholarly journals Disentangling the determinants of transposable elements dynamics in vertebrate genomes using empirical evidences and simulations

2020 ◽  
Author(s):  
Yann Bourgeois ◽  
Robert Ruggiero ◽  
Imtiyaz Hariyani ◽  
Stéphane Boissinot
Keyword(s):  
Transposable Elements ◽  
Demographic History ◽  
Ltr Retrotransposons ◽  
Frequency Spectra ◽  
Dna Transposons ◽  
Genomic Landscape ◽  
Demographic Processes ◽  
History Of ◽  
Recent Phase ◽  
Positive Correlations

AbstractBackgroundThe interactions between transposable elements (TEs) and their hosts constitute one of the most profound co-evolutionary processes found in nature. The population dynamics of TEs depends on factors specific to each TE families, such as the rate of transposition and insertional preference, the demographic history of the host and the genomic landscape. How these factors interact has yet to be investigated holistically. Here we are addressing this question in the green anole (Anolis carolinensis) whose genome contains an extraordinary diversity of TEs (including non-LTR retrotransposons, SINEs, LTR-retrotransposons and DNA transposons).ResultsWe observe a positive correlation between recombination rate and TEs frequencies and densities for LINEs, SINEs and DNA transposons. For these elements, there was a clear impact of demography on TE frequency and abundance, with a loss of polymorphic elements and skewed frequency spectra in recently expanded populations. On the other hand, some LTR-retrotransposons displayed patterns consistent with a very recent phase of intense amplification. To determine how demography, genomic features and intrinsic properties of TEs interact we ran simulations using SLiM3. We determined that i) short TE insertions are not strongly counter-selected, but long ones are, ii) neutral demographic processes, linked selection and preferential insertion may explain positive correlations between average TE frequency and recombination, iii) TE insertions are unlikely to have been massively recruited in recent adaptation..ConclusionsWe demonstrate that deterministic and stochastic processes have different effects on categories of TEs and that a combination of empirical analyses and simulations can disentangle the effects of these processes.

scholarly journals Dynamic Sampling Bias and Overdispersion Induced by Skewed Offspring Distributions

Genetics ◽  
2021 ◽  
Author(s):  
Takashi Okada ◽  
Oskar Hallatschek
Keyword(s):  
Allele Frequency ◽  
Evolutionary Dynamics ◽  
Statistical Tests ◽  
Demographic History ◽  
Sampling Bias ◽  
Coarse Grained ◽  
Frequency Spectra ◽  
Scaling Hypothesis ◽  
Frequency Fluctuations ◽  
Dynamic Sampling

Abstract Natural populations often show enhanced genetic drift consistent with a strong skew in their offspring number distribution. The skew arises because the variability of family sizes is either inherently strong or amplified by population expansions. The resulting allele-frequency fluctuations are large and, therefore, challenge standard models of population genetics, which assume sufficiently narrow offspring distributions. While the neutral dynamics backward in time can be readily analyzed using coalescent approaches, we still know little about the effect of broad offspring distributions on the forward-in-time dynamics, especially with selection. Here, we employ an asymptotic analysis combined with a scaling hypothesis to demonstrate that over-dispersed frequency trajectories emerge from the competition of conventional forces, such as selection or mutations, with an emerging time-dependent sampling bias against the minor allele. The sampling bias arises from the characteristic time-dependence of the largest sampled family size within each allelic type. Using this insight, we establish simple scaling relations for allele-frequency fluctuations, fixation probabilities, extinction times, and the site frequency spectra that arise when offspring numbers are distributed according to a power law n−(1+α). To demonstrate that this coarse-grained model captures a wide variety of evolutionary dynamics, we validate our results in traveling waves, where the phenomenon of ’gene surfing’ can produce any exponent 1 &lt; α &lt; 2. We argue that the concept of a dynamic sampling bias is useful to develop both intuition and statistical tests for the unusual dynamics of populations with skewed offspring distributions, which can confound commonly used tests for selection or demographic history.

scholarly journals Cattle demographic history modelled from autosomal sequence variation

2010 ◽  
Vol 365 (1552) ◽  
pp. 2531-2539 ◽  
Author(s):  
Caitriona Murray ◽  
Emilia Huerta-Sanchez ◽  
Fergal Casey ◽  
Daniel G. Bradley
Keyword(s):  
South Asian ◽  
Sequence Variation ◽  
Bos Taurus ◽  
Demographic History ◽  
Bos Indicus ◽  
Frequency Spectra ◽  
Demographic Models ◽  
History Of ◽  
Best Fitting ◽  
Fitting Model

The phylogeography of cattle genetic variants has been extensively described and has informed the history of domestication. However, there remains a dearth of demographic models inferred from such data. Here, we describe sequence diversity at 37 000 bp sampled from 17 genes in cattle from Africa, Europe and India. Clearly distinct population histories are suggested between Bos indicus and Bos taurus , with the former displaying higher diversity statistics. We compare the unfolded site frequency spectra in each to those simulated using a diffusion approximation method and build a best-fitting model of past demography. This implies an earlier, possibly glaciation-induced population bottleneck in B. taurus ancestry with a later, possibly domestication-associated demographic constriction in B. indicus . Strikingly, the modelled indicine history also requires a majority secondary admixture from the South Asian aurochs, indicating a complex, more diffuse domestication process. This perhaps involved multiple domestications and/or introgression from wild oxen to domestic herds; the latter is plausible from archaeological evidence of contemporaneous wild and domestic remains across different regions of South Asia.

Heart Rate Variability, Emotions, and Music

2010 ◽  
Vol 24 (2) ◽  
pp. 112-119 ◽  
Author(s):  
F. Riganello ◽  
A. Candelieri ◽  
M. Quintieri ◽  
G. Dolce
Keyword(s):  
Data Mining ◽  
Heart Rate ◽  
Heart Rate Variability ◽  
Vegetative State ◽  
Low Frequency ◽  
Emotional Reactions ◽  
Heart Beat ◽  
Healthy Controls ◽  
Frequency Spectra ◽  
Emotional Value

The purpose of the study was to identify significant changes in heart rate variability (an emerging descriptor of emotional conditions; HRV) concomitant to complex auditory stimuli with emotional value (music). In healthy controls, traumatic brain injured (TBI) patients, and subjects in the vegetative state (VS) the heart beat was continuously recorded while the subjects were passively listening to each of four music samples of different authorship. The heart rate (parametric and nonparametric) frequency spectra were computed and the spectra descriptors were processed by data-mining procedures. Data-mining sorted the nu_lf (normalized parameter unit of the spectrum low frequency range) as the significant descriptor by which the healthy controls, TBI patients, and VS subjects’ HRV responses to music could be clustered in classes matching those defined by the controls and TBI patients’ subjective reports. These findings promote the potential for HRV to reflect complex emotional stimuli and suggest that residual emotional reactions continue to occur in VS. HRV descriptors and data-mining appear applicable in brain function research in the absence of consciousness.

Right-Hemisphere Specialization for Contour Grouping

2014 ◽  
Vol 61 (5) ◽  
pp. 331-339 ◽  
Author(s):  
Gregor Volberg
Keyword(s):  
Right Hemisphere ◽  
Contour Detection ◽  
Global Processing ◽  
Detection Accuracy ◽  
Frequency Spectra ◽  
Visual Hemifield ◽  
Spatial Frequencies ◽  
A Chain ◽  
The Right ◽  
Hemisphere Specialization

Previous studies often revealed a right-hemisphere specialization for processing the global level of compound visual stimuli. Here we explore whether a similar specialization exists for the detection of intersected contours defined by a chain of local elements. Subjects were presented with arrays of randomly oriented Gabor patches that could contain a global path of collinearly arranged elements in the left or in the right visual hemifield. As expected, the detection accuracy was higher for contours presented to the left visual field/right hemisphere. This difference was absent in two control conditions where the smoothness of the contour was decreased. The results demonstrate that the contour detection, often considered to be driven by lateral coactivation in primary visual cortex, relies on higher-level visual representations that differ between the hemispheres. Furthermore, because contour and non-contour stimuli had the same spatial frequency spectra, the results challenge the view that the right-hemisphere advantage in global processing depends on a specialization for processing low spatial frequencies.

Harmonics in frequency spectra: a contribution to differential diagnosis of tremor

2007 ◽  
Vol 34 (S 2) ◽  
Author(s):  
G Ellrichmann ◽  
J Jamrozy ◽  
A Hoffmann ◽  
PH Kraus
Keyword(s):  
Differential Diagnosis ◽  
Frequency Spectra
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