scholarly journals Signatures of Introgression across the Allele Frequency Spectrum

2020 ◽  
Author(s):  
Simon H Martin ◽  
William Amos
Keyword(s):  
Frequency Spectrum ◽  
Empirical Data ◽  
Low Frequency ◽  
Genomic Data ◽  
Simple Extension ◽  
Allele Sharing ◽  
Large Parameter ◽  
Low Frequencies ◽  
Allele Frequency Spectrum ◽  
Large Parameter Space

Abstract The detection of introgression from genomic data is transforming our view of species and the origins of adaptive variation. Among the most widely used approaches to detect introgression is the so-called ABBA–BABA test or D-statistic, which identifies excess allele sharing between nonsister taxa. Part of the appeal of D is its simplicity, but this also limits its informativeness, particularly about the timing and direction of introgression. Here we present a simple extension, D frequency spectrum or DFS, in which D is partitioned according to the frequencies of derived alleles. We use simulations over a large parameter space to show how DFS carries information about various factors. In particular, recent introgression reliably leads to a peak in DFS among low-frequency derived alleles, whereas violation of model assumptions can lead to a lack of signal at low frequencies. We also reanalyze published empirical data from six different animal and plant taxa, and interpret the results in the light of our simulations, showing how DFS provides novel insights. We currently see DFS as a descriptive tool that will augment both simple and sophisticated tests for introgression, but in the future it may be usefully incorporated into probabilistic inference frameworks.

scholarly journals Signatures of introgression across the allele frequency spectrum

2020 ◽  
Author(s):  
Simon H. Martin ◽  
William Amos
Keyword(s):  
Frequency Spectrum ◽  
Empirical Data ◽  
Low Frequency ◽  
Genomic Data ◽  
Simple Extension ◽  
Allele Sharing ◽  
Large Parameter ◽  
Low Frequencies ◽  
Allele Frequency Spectrum ◽  
Large Parameter Space

ABSTRCTThe detection of introgression from genomic data is transforming our view of species and the origins of adaptive variation. Among the most widely used approaches to detect introgression is the so-called ABBA BABA test or D statistic, which identifies excess allele sharing between non-sister taxa. Part of the appeal of D is its simplicity, but this also limits its informativeness, particularly about the timing and direction of introgression. Here we present a simple extension, D frequency spectrum or DFS, in which D is partitioned according to the frequencies of derived alleles. We use simulations over a large parameter space to show how DFS caries information about various factors. In particular, recent introgression reliably leads to a peak in DFS among low-frequency derived alleles, whereas violation of model assumptions can lead to a lack of signal at low-frequencies. We also reanalyse published empirical data from six different animal and plant taxa, and interpret the results in the light of our simulations, showing how DFS provides novel insights. We currently see DFS as a descriptive tool that will augment both simple and sophisticated tests for introgression, but in the future it may be usefully incorporated into probabilistic inference frameworks.

scholarly journals West Asian sources of the Eurasian component in Ethiopians: a reassessment

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Ludovica Molinaro ◽  
Francesco Montinaro ◽  
Burak Yelmen ◽  
Davide Marnetto ◽  
Doron M. Behar ◽  
...  
Keyword(s):  
Allele Frequency ◽  
Frequency Spectrum ◽  
Mediterranean Area ◽  
Genetic Component ◽  
Single Site ◽  
Allele Sharing ◽  
Population Movements ◽  
Genomic Signatures ◽  
Allele Frequency Spectrum ◽  
Source Populations

AbstractThe presence of genomic signatures of Eurasian origin in contemporary Ethiopians has been reported by several authors and estimated to have arrived in the area from 3000 years ago. Several studies reported plausible source populations for such a signature, using haplotype based methods on modern data or single-site methods on modern or ancient data. These studies did not reach a consensus and suggested an Anatolian or Sardinia-like proxy, broadly Levantine or Neolithic Levantine as possible sources. We demonstrate, however, that the deeply divergent, autochthonous African component which accounts for ~50% of most contemporary Ethiopian genomes, affects the overall allele frequency spectrum to an extent that makes it hard to control for it and, at once, to discern between subtly different, yet important, Eurasian sources (such as Anatolian or Levant Neolithic ones). Here we re-assess pattern of allele sharing between the Eurasian component of Ethiopians (here called “NAF” for Non African) and ancient and modern proxies. Our results unveil a genomic legacy that may connect the Eurasian genetic component of contemporary Ethiopians with Sea People and with population movements that affected the Mediterranean area and the Levant after the fall of the Minoan civilization.

scholarly journals On the prospect of identifying adaptive loci in recently bottlenecked populations

2014 ◽  
Author(s):  
Yu-Ping Poh ◽  
Vera S Domingues ◽  
Hopi Hoekstra ◽  
Jeffrey Jensen
Keyword(s):  
Frequency Spectrum ◽  
Population Genetic ◽  
Null Model ◽  
Large Parameter ◽  
Independent Evidence ◽  
Standing Variation ◽  
In The Wild ◽  
Site Frequency Spectrum ◽  
Genomic Regions ◽  
Large Parameter Space

Identifying adaptively important loci in recently bottlenecked populations?be it natural selection acting on a population following the colonization of novel habitats in the wild, or artificial selection during the domestication of a breed?remains a major challenge. Here we report the results of a simulation study examining the performance of available population-genetic tools for identifying genomic regions under selection. To illustrate our findings, we examined the interplay between selection and demography in two species of Peromyscus mice, for which we have independent evidence of selection acting on phenotype as well as functional evidence identifying the underlying genotype. With this unusual information, we tested whether population-genetic-based approaches could have been utilized to identify the adaptive locus. Contrary to published claims, we conclude that the use of the background site frequency spectrum as a null model is largely ineffective in bottlenecked populations. Results are quantified both for site frequency spectrum and linkage disequilibrium-based predictions, and are found to hold true across a large parameter space that encompasses many species and populations currently under study. These results suggest that the genomic footprint left by selection on both new and standing variation in strongly bottlenecked populations will be difficult, if not impossible, to find using current approaches.

scholarly journals West Asian sources of the Eurasian component in Ethiopians: a reassessment

2019 ◽  
Author(s):  
Ludovica Molinaro ◽  
Francesco Montinaro ◽  
Toomas Kivisild ◽  
Luca Pagani
Keyword(s):  
Gene Flow ◽  
Allele Frequency ◽  
Frequency Spectrum ◽  
Mediterranean Area ◽  
Genotype Data ◽  
Allele Sharing ◽  
Population Movements ◽  
Allele Frequency Spectrum ◽  
Population Source ◽  
Genome Scale

SummaryPrevious genome-scale studies of populations living today in Ethiopia have found evidence of recent gene flow from an Eurasian source, dating to the last 3,000 years1,2,3,4. Haplotype1 and genotype data based analyses of modern2,4 and ancient data (aDNA)3,5 have considered Sardinia-like proxy2, broadly Levantine1,4 or Neolithic Levantine3 populations as a range of possible sources for this gene flow. Given the ancient nature of this gene flow and the extent of population movements and replacements that affected West Asia in the last 3000 years, aDNA evidence would seem as the best proxy for determining the putative population source. We demonstrate, however, that the deeply divergent, autochthonous African component which accounts for ∼50% of most contemporary Ethiopian genomes, affects the overall allele frequency spectrum to an extent that makes it hard to control for it and, at once, to discern between subtly different, yet important, Eurasian sources (such as Anatolian or Levant Neolithic ones). Here we re-assess pattern of allele sharing between the Eurasian component of Ethiopians (here called “NAF” for Non African) and ancient and modern proxies area after having extracted NAF from Ethiopians through ancestry deconvolution, and unveil a genomic signature compatible with population movements that affected the Mediterranean area and the Levant after the fall of the Minoan civilization.

Collision enhanced hyper-damping in nonlinear elastic metamaterial

2022 ◽  
Author(s):  
Miao Yu ◽  
Xin Fang ◽  
Dianlong Yu ◽  
Jihong Wen ◽  
Li Cheng
Keyword(s):  
Vibration Suppression ◽  
Vibration Reduction ◽  
Low Frequency ◽  
Strong Nonlinearity ◽  
Large Parameter ◽  
Damping Effect ◽  
Elastic Metamaterials ◽  
Proper Design ◽  
Nonlinear Elastic ◽  
Large Parameter Space

Abstract Nonlinear elastic metamaterial, a topic which has attracted extensive attention in recent years, can enable broadband vibration reduction under relatively large amplitude. The combination of damping and strong nonlinearity in metamaterials may entail auxetic effects and offer the capability for low-frequency and broadband vibration reduction. However, there exists a clear lack of proper design methods as well as a deficiency in understanding properties arising from this concept. To tackle this problem, this paper numerically demonstrates that the nonlinear elastic metamaterials, consisting of sandwich damping layers and collision resonators, can generate very robust hyper-damping effect, conducive to efficient and broadband vibration suppression. The collision-enhanced hyper damping is persistently present in a large parameter space, ranging from small to large amplitudes, and for small and large damping coefficient. The achieved robust effects greatly enlarge the application scope of nonlinear metamaterials. We report the design concept, properties and mechanisms of the hyper-damping and its effect on vibration transmission. This paper reveals new properties offered by nonlinear elastic metamaterials, and offers a robust method for achieving efficient low-frequency and broadband vibration suppression.

scholarly journals Earless toads sense low frequencies but miss the high notes

2017 ◽  
Vol 284 (1864) ◽  
pp. 20171670 ◽  
Author(s):  
Molly C. Womack ◽  
Jakob Christensen-Dalsgaard ◽  
Luis A. Coloma ◽  
Juan C. Chaparro ◽  
Kim L. Hoke
Keyword(s):  
High Frequency ◽  
Species Differences ◽  
Low Frequency ◽  
Auditory Brainstem ◽  
Low Frequencies ◽  
Hearing Sensitivity ◽  
Sensory Pathways ◽  
Airborne Sound ◽  
Vibrational Sensitivity ◽  
Species Specific

Sensory losses or reductions are frequently attributed to relaxed selection. However, anuran species have lost tympanic middle ears many times, despite anurans' use of acoustic communication and the benefit of middle ears for hearing airborne sound. Here we determine whether pre-existing alternative sensory pathways enable anurans lacking tympanic middle ears (termed earless anurans) to hear airborne sound as well as eared species or to better sense vibrations in the environment. We used auditory brainstem recordings to compare hearing and vibrational sensitivity among 10 species (six eared, four earless) within the Neotropical true toad family (Bufonidae). We found that species lacking middle ears are less sensitive to high-frequency sounds, however, low-frequency hearing and vibrational sensitivity are equivalent between eared and earless species. Furthermore, extratympanic hearing sensitivity varies among earless species, highlighting potential species differences in extratympanic hearing mechanisms. We argue that ancestral bufonids may have sufficient extratympanic hearing and vibrational sensitivity such that earless lineages tolerated the loss of high frequency hearing sensitivity by adopting species-specific behavioural strategies to detect conspecifics, predators and prey.

A waveform inversion technique for measuring elastic wave attenuation in cylindrical bars

Geophysics ◽  
1992 ◽  
Vol 57 (6) ◽  
pp. 854-859 ◽  
Author(s):  
Xiao Ming Tang
Keyword(s):  
Elastic Wave ◽  
Wave Attenuation ◽  
Waveform Inversion ◽  
Finite Size ◽  
Low Frequency ◽  
Frequency Range ◽  
Multiple Reflections ◽  
Low Frequencies ◽  
The Time Domain ◽  
Attenuation Values

A new technique for measuring elastic wave attenuation in the frequency range of 10–150 kHz consists of measuring low‐frequency waveforms using two cylindrical bars of the same material but of different lengths. The attenuation is obtained through two steps. In the first, the waveform measured within the shorter bar is propagated to the length of the longer bar, and the distortion of the waveform due to the dispersion effect of the cylindrical waveguide is compensated. The second step is the inversion for the attenuation or Q of the bar material by minimizing the difference between the waveform propagated from the shorter bar and the waveform measured within the longer bar. The waveform inversion is performed in the time domain, and the waveforms can be appropriately truncated to avoid multiple reflections due to the finite size of the (shorter) sample, allowing attenuation to be measured at long wavelengths or low frequencies. The frequency range in which this technique operates fills the gap between the resonant bar measurement (∼10 kHz) and ultrasonic measurement (∼100–1000 kHz). By using the technique, attenuation values in a PVC (a highly attenuative) material and in Sierra White granite were measured in the frequency range of 40–140 kHz. The obtained attenuation values for the two materials are found to be reliable and consistent.

Methods to isolate retrograde and prograde Rayleigh-wave signals

2019 ◽  
Vol 219 (2) ◽  
pp. 975-994 ◽  
Author(s):  
Gabriel Gribler ◽  
T Dylan Mikesell
Keyword(s):  
Rayleigh Wave ◽  
Time Domain ◽  
Fundamental Mode ◽  
Poisson Ratio ◽  
Low Frequency ◽  
Wave Dispersion ◽  
Low Frequencies ◽  
Retrograde Motion ◽  
Mode Identification ◽  
Time Frequency

SUMMARY Estimating shear wave velocity with depth from Rayleigh-wave dispersion data is limited by the accuracy of fundamental and higher mode identification and characterization. In many cases, the fundamental mode signal propagates exclusively in retrograde motion, while higher modes propagate in prograde motion. It has previously been shown that differences in particle motion can be identified with multicomponent recordings and used to separate prograde from retrograde signals. Here we explore the domain of existence of prograde motion of the fundamental mode, arising from a combination of two conditions: (1) a shallow, high-impedance contrast and (2) a high Poisson ratio material. We present solutions to isolate fundamental and higher mode signals using multicomponent recordings. Previously, a time-domain polarity mute was used with limited success due to the overlap in the time domain of fundamental and higher mode signals at low frequencies. We present several new approaches to overcome this low-frequency obstacle, all of which utilize the different particle motions of retrograde and prograde signals. First, the Hilbert transform is used to phase shift one component by 90° prior to summation or subtraction of the other component. This enhances either retrograde or prograde motion and can increase the mode amplitude. Secondly, we present a new time–frequency domain polarity mute to separate retrograde and prograde signals. We demonstrate these methods with synthetic and field data to highlight the improvements to dispersion images and the resulting dispersion curve extraction.

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.

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