Optimal Moments for the Analysis of Peculiar Velocity Surveys

We present a new method for the analysis of peculiar velocity surveys which removes contributions to velocities from small scale, nonlinear velocity modes while retaining information about large scale motions. Our method utilizes Karhunen--Lo\`eve methods of data compression to construct a set of moments out of the velocities which are minimally sensitive to small scale power. The set of moments are then used in a likelihood analysis. We develop criteria for the selection of moments, as well as a statistic to quantify the overall sensitivity of a set of moments to small scale power. Although we discuss our method in the context of peculiar velocity surveys, it may also prove useful in other situations where data filtering is required.Comment: 25 Pages, 3 figures. Submitted to Ap

Optimal Moments for the Analysis of Peculiar Velocity Surveys II: Testing

Analyses of peculiar velocity surveys face several challenges, including low signal--to--noise in individual velocity measurements and the presence of small--scale, nonlinear flows. This is the second in a series of papers in which we describe a new method of overcoming these problems by using data compression as a filter with which to separate large--scale, linear flows from small--scale noise that can bias results. We demonstrate the effectiveness of our method using realistic catalogs of galaxy velocities drawn from N--body simulations. Our tests show that a likelihood analysis of simulated catalogs that uses all of the information contained in the peculiar velocities results in a bias in the estimation of the power spectrum shape parameter $\Gamma$ and amplitude $\beta$, and that our method of analysis effectively removes this bias. We expect that this new method will cause peculiar velocity surveys to re--emerge as a useful tool to determine cosmological parameters.Comment: 28 pages, 9 figure

Tapinoma nigerrimum as safeguard for Italian myrmecofauna against Argentine ant

The Hurst effect plays an important role in many areas such as physics, climate and finance. It describes the anomalous growth of range and constrains the behavior and predictability of these systems. The Hurst effect is frequently taken to be synonymous with Long-Range Dependence (LRD) and is typically assumed to be produced by a stationary stochastic process which has infinite memory. However, infinite memory appears to be at odds with the Markovian nature of most physical laws while the stationarity assumption lacks robustness. Here we use Lorenz's paradigmatic chaotic model to show that regime behavior can also cause the Hurst effect. By giving an alternative, parsimonious, explanation using nonstationary Markovian dynamics, our results question the common belief that the Hurst effect necessarily implies a stationary infinite memory process. We also demonstrate that our results can explain atmospheric variability without the infinite memory previously thought necessary and are consistent with climate model simulations

Culture creates genetic structure in the Caucasus: Autosomal, mitochondrial, and Y-chromosomal variation in Daghestan

<p>Abstract</p> <p>Background</p> <p>Near the junction of three major continents, the Caucasus region has been an important thoroughfare for human migration. While the Caucasus Mountains have diverted human traffic to the few lowland regions that provide a gateway from north to south between the Caspian and Black Seas, highland populations have been isolated by their remote geographic location and their practice of patrilocal endogamy. We investigate how these cultural and historical differences between highland and lowland populations have affected patterns of genetic diversity. We test 1) whether the highland practice of patrilocal endogamy has generated sex-specific population relationships, and 2) whether the history of migration and military conquest associated with the lowland populations has left Central Asian genes in the Caucasus, by comparing genetic diversity and pairwise population relationships between Daghestani populations and reference populations throughout Europe and Asia for autosomal, mitochondrial, and Y-chromosomal markers.</p> <p>Results</p> <p>We found that the highland Daghestani populations had contrasting histories for the mitochondrial DNA and Y-chromosome data sets. Y-chromosomal haplogroup diversity was reduced among highland Daghestani populations when compared to other populations and to highland Daghestani mitochondrial DNA haplogroup diversity. Lowland Daghestani populations showed Turkish and Central Asian affinities for both mitochondrial and Y-chromosomal data sets. Autosomal population histories are strongly correlated to the pattern observed for the mitochondrial DNA data set, while the correlation between the mitochondrial DNA and Y-chromosome distance matrices was weak and not significant.</p> <p>Conclusion</p> <p>The reduced Y-chromosomal diversity exhibited by highland Daghestani populations is consistent with genetic drift caused by patrilocal endogamy. Mitochondrial and Y-chromosomal phylogeographic comparisons indicate a common Near Eastern origin of highland populations. Lowland Daghestani populations show varying influence from Near Eastern and Central Asian populations.</p

Recently integrated Alu elements and human genomic diversity

A comprehensive analysis of two Alu Y lineage subfamilies was undertaken to assess Alu-associated genomic diversity and identify new Alu insertion polymorphisms for the study of human population genetics. Recently integrated Alu elements (283) from the Yg6 and Yi6 subfamilies were analyzed by polymerase chain reaction (PCR), and 25 of the loci analyzed were polymorphic for insertion presence/absence within the genomes of a diverse array of human populations. These newly identified Alu insertion polymorphisms will be useful tools for the study of human genomic diversity. Our screening of the Alu insertion loci also resulted in the recovery of several young Alu elements that resided at orthologous positions in nonhuman primate genomes. Sequence analysis demonstrated these young Alu insertions were the products of gene conversion events of older, preexisting Alu elements or independent parallel forward insertions of older Alu elements in the same short genomic region. The level of gene conversion between Alu elements suggests that it may have an influence on the single nucleotide polymorphism within Alu elements in the genome. We have also identified two genomic deletions associated with the retroposition and insertion of Alu Y lineage elements into the human genome. This type of Alu retroposition-mediated genomic deletion is a novel source of lineage-specific evolution within primate genomes

Mobile element scanning (ME-Scan) by targeted high-throughput sequencing

<p>Abstract</p> <p>Background</p> <p>Mobile elements (MEs) are diverse, common and dynamic inhabitants of nearly all genomes. ME transposition generates a steady stream of polymorphic genetic markers, deleterious and adaptive mutations, and substrates for further genomic rearrangements. Research on the impacts, population dynamics, and evolution of MEs is constrained by the difficulty of ascertaining rare polymorphic ME insertions that occur against a large background of pre-existing fixed elements and then genotyping them in many individuals.</p> <p>Results</p> <p>Here we present a novel method for identifying nearly all insertions of a ME subfamily in the whole genomes of multiple individuals and simultaneously genotyping (for presence or absence) those insertions that are variable in the population. We use ME-specific primers to construct DNA libraries that contain the junctions of all ME insertions of the subfamily, with their flanking genomic sequences, from many individuals. Individual-specific "index" sequences are designed into the oligonucleotide adapters used to construct the individual libraries. These libraries are then pooled and sequenced using a ME-specific sequencing primer. Mobile element insertion loci of the target subfamily are uniquely identified by their junction sequence, and all insertion junctions are linked to their individual libraries by the corresponding index sequence. To test this method's feasibility, we apply it to the human <it>AluYb8 </it>and <it>AluYb9 </it>subfamilies. In four individuals, we identified a total of 2,758 <it>AluYb8 </it>and <it>AluYb9 </it>insertions, including nearly all those that are present in the reference genome, as well as 487 that are not. Index counts show the sequenced products from each sample reflect the intended proportions to within 1%. At a sequencing depth of 355,000 paired reads per sample, the sensitivity and specificity of ME-Scan are both approximately 95%.</p> <p>Conclusions</p> <p>Mobile Element Scanning (ME-Scan) is an efficient method for quickly genotyping mobile element insertions with very high sensitivity and specificity. In light of recent improvements to high-throughput sequencing technology, it should be possible to employ ME-Scan to genotype insertions of almost any mobile element family in many individuals from any species.</p

Mobile element scanning (ME-Scan) identifies thousands of novel Alu insertions in diverse human populations

Alu retrotransposons are the most numerous and active mobile elements in humans, causing genetic disease and creating genomic diversity. Mobile element scanning (ME-Scan) enables comprehensive and affordable identification of mobile element insertions (MEI) using targeted high-throughput sequencing of multiplexed MEI junction libraries. In a single experiment, ME-Scan identifies nearly all AluYb8 and AluYb9 elements, with high sensitivity for both rare and common insertions, in 169 individuals of diverse ancestry. ME-Scan detects heterozygous insertions in single individuals with 91% sensitivity. Insertion presence or absence states determined by ME-Scan are 95% concordant with those determined by locus-specific PCR assays. By sampling diverse populations from Africa, South Asia, and Europe, we are able to identify 5799 Alu insertions, including 2524 novel ones, some of which occur in exons. Sub-Saharan populations and a Pygmy group in particular carry numerous intermediate-frequency Alu insertions that are absent in non-African groups. There is a significant dearth of exon-interrupting insertions among common Alu polymorphisms, but the density of singleton Alu insertions is constant across exonic and nonexonic regions. In one case, a validated novel singleton Alu interrupts a proteincoding exon of FAM187B. This implies that exonic Alu insertions are generally deleterious and thus eliminated by natural selection, but not so quickly that they cannot be observed as extremely rare variants. © 2013, Published by Cold Spring Harbor Laboratory Press

Response to “Limitations in the Hilbert Transform Approach to Locating Solar Cycle Terminators” by R. Booth

Booth (Solar Phys.296, 108, 2021; hereafter B21) is essentially a critique of the Hilbert transform techniques used in our paper (Leamon et al., Solar Phys.295, 36, 2020; hereafter L20) to predict the termination of solar cycles. Here we respond to his arguments; our methodology and parameter choices do extract a mathematically robust signature of terminators from the historical sunspot record. We agree that the attempt in L20 to extrapolate beyond the sunspot record gives a failed prediction for the next terminator of May 2020, and we identify both a possible cause and remedy here. However, we disagree with the B21 assessment that the likely termination of Solar Cycle 24 is two years after the date predicted in L20, and we show why

Overlapping Magnetic Activity Cycles and the Sunspot Number: Forecasting Sunspot Cycle 25 Amplitude

The Sun exhibits a well-observed modulation in the number of spots on its disk over a period of about 11 years. From the dawn of modern observational astronomy, sunspots have presented a challenge to understanding—their quasi-periodic variation in number, first noted 175 years ago, has stimulated community-wide interest to this day. A large number of techniques are able to explain the temporal landmarks, (geometric) shape, and amplitude of sunspot “cycles,” however, forecasting these features accurately in advance remains elusive. Recent observationally-motivated studies have illustrated a relationship between the Sun’s 22-year (Hale) magnetic cycle and the production of the sunspot cycle landmarks and patterns, but not the amplitude of the sunspot cycle. Using (discrete) Hilbert transforms on more than 270 years of (monthly) sunspot numbers we robustly identify the so-called “termination” events that mark the end of the previous 11-yr sunspot cycle, the enhancement/acceleration of the present cycle, and the end of 22-yr magnetic activity cycles. Using these we extract a relationship between the temporal spacing of terminators and the magnitude of sunspot cycles. Given this relationship and our prediction of a terminator event in 2020, we deduce that sunspot Solar Cycle 25 could have a magnitude that rivals the top few since records began. This outcome would be in stark contrast to the community consensus estimate of sunspot Solar Cycle 25 magnitude