Numerical and experimental comparison among a new hybrid FT-music technique and existing algorithms for through-the-wall radar imaging

A fast low-cost through-the-wall radar imaging (TWRI) system, based on a vector network analyzer (VNA), a couple of switches and an array of Vivaldi antennas, has been designed, realized, and tested. To solve the TWRI inversion problem, an original theoretical modeling for a class of TWRI techniques whose basic functions are the cross-range Fourier transform (FT) of the scattered field and its covariance operator has been proposed. Using these functions, four conventional algorithms, namely the delay and sum (DAS), the FT, the multiple signal classification (MUSIC), the hybrid DAS-MUSIC and a new algorithm, the hybrid FT-MUSIC, have been derived. All these techniques have been implemented and their accuracy and field of view have been tested on canonical scatterers. Then, the algorithms have been applied to measured data collected in different scenarios constituted by a metallic bar or a human subject in the absence and in the presence of a wall between the antenna and the considered targets. Using the proposed TWRI system, it has been possible to detect a subject located up to 5-m away from the radar antenna array through a tuff wall. The proposed FT-MUSIC algorithm has evidenced performances similar to those of the DAS-MUSIC but with significantly lower execution times. Finally, FT-MUSIC performances in terms of field of view and immunity to disturbances are better compared to those of the MUSIC algorithm

Ethnic fragmentation and degree of urbanization strongly affect the discrimination power of Y-STR haplotypes in central Sahel

Y chromosome short tandem repeats (Y-STRs) are commonly used to identify male lineages for investigative and judicial purposes and could represent the only source of male-specific genetic information from unbalanced female-male mixtures. The Yfiler Plus multiplex, which includes twenty conventional and seven rapidly-mutating Y-STRs, represents the most discriminating patrilineal system commercially available to date. Over the past five years, this multiplex has been used to analyze several Eurasian populations, with a reported discrimination capacity (DC) approaching or corresponding to the highest possible value. However, despite the inclusion of rapidly mutating Y-STRs, extensive haplotype sharing was still reported for some African populations due to a number of different factors affecting the effective population size. In the present study, we analyzed 27 Y-STRs included in the Yfiler Plus multiplex and 82 Y-SNPs in central Sahel (northern Cameroon and western Chad), an African region characterized by a strong ethnic fragmentation and linguistic diversity. We evaluated the effects of population sub-structuring on genetic diversity by stratifying a sample composed of 431 males according to their ethnicity (44 different ethnic groups) and urbanization degree (four villages and four towns). Overall, we observed a low discrimination capacity (DC = 0.90), with 71 subjects (16.5 %) sharing 27 Y-STR haplotypes. Haplotype sharing was essentially limited to subjects with the same binary haplogroup, coming from the same location and belonging to the same ethnic group. Haplotype sharing was much higher in rural areas (average DC = 0.83) than urban settlements (average DC = 0.96) with a significant correlation between DC and census size (r = 0.89; p = 0.003). Notably, we found that genetic differentiation between villages from the same country (ΦST = 0.14) largely exceeded that found among countries (ΦST = 0.02). These findings have important implications for the choice of the appropriate reference population database to evaluate the statistical relevance of forensic Y-haplotype matches

The peopling of the last Green Sahara revealed by high-coverage resequencing of trans-Saharan patrilineages

Little is known about the peopling of the Sahara during the Holocene climatic optimum, when the desert was replaced by a fertile environment

Genetic history of Cambridgeshire before and after the Black Death.

The extent of the devastation of the Black Death pandemic (1346-1353) on European populations is known from documentary sources and its bacterial source illuminated by studies of ancient pathogen DNA. What has remained less understood is the effect of the pandemic on human mobility and genetic diversity at the local scale. Here, we report 275 ancient genomes, including 109 with coverage >0.1×, from later medieval and postmedieval Cambridgeshire of individuals buried before and after the Black Death. Consistent with the function of the institutions, we found a lack of close relatives among the friars and the inmates of the hospital in contrast to their abundance in general urban and rural parish communities. While we detect long-term shifts in local genetic ancestry in Cambridgeshire, we find no evidence of major changes in genetic ancestry nor higher differentiation of immune loci between cohorts living before and after the Black Death

Dynamics of gene conversion in human MSY palindromes

The Male Specific region of the human Y chromosome (MSY) is characterized by the presence of 8 near identical 'pseudo-diploid' sequences, called palindromes, which are designated as P1–P8. Palindromes are composed of inverted repeats (palindrome arms), separated by a non-duplicated spacer. Although these structures originated in a non-recombining context, they show evidence of a strong recombinational activity. Palindromes exhibit more than 99.94% sequence identity between arms, due to the homogenizing effect of arm-to-arm gene conversion (GC), a type of recombination which involves the non-reciprocal transfer of genetic information from a “donor” sequence to a highly similar “acceptor” sequence. The independent appearance of these paralogue structures in sex chromosomes of many different species suggests that they may have an important biological meaning. It has been hypothesized that the palindromic organization and the establishment of inter-paralogs gene conversion have a strong adaptive significance since the arm-to-arm GC may allow double-strand break repair and the efficient removal of deleterious mutations. Thus, it has been proposed that this mechanism was acquired to maintain the structural integrity of multi-copy genes involved in the male-fertility. Moreover, it has been hypothesized that gene conversion evolved as a mechanism to retain the ancestral state of sequences: a de novo mutation in a palindrome arm is preferentially back mutated to the ancestral state rather than transmitted to the other arm. In this contest, to gain new insights into the dynamics of gene conversion within human Y chromosome palindromes, we performed next-generation sequencing (depth >50×) of 3 palindromes (P6, P7 and P8) in 157 samples, chosen to represent the most divergent evolutionary lineages of the MSY. In this analysis, we overcame the problem of the inaccurate mapping of the duplicated reads, and we performed a sequencing depth analysis to detect deletions or duplications which may result in genotype miscalling. We identified more than 200 paralogue sequence variants and 140 GC events. Mapping these GC events across a stable and non-ambiguous Y chromosome phylogeny enabled the calculation of a precise Y-Y gene conversion rate for each palindrome and the assessment of the direction of the recombinational activity. From these analyses we conclude that MSY palindromes have an evolutionary pattern more complex than previously thought

Dynamics of gene conversion in human Y-chromosome palindromes

The Male Specific region of the human Y chromosome (MSY) is characterized by the presence of eight massive palindromes. Each palindrome is composed of two large arms separated by a non-duplicated spacer. These elements exhibit an arm-to-arm sequence identity >99.9%, due to gene conversion (GC) events between them. The effect of GC on the genetic diversity of palindromes, as well as its rate and extension, remain largely unexplored. To gain new insights into the evolutionary dynamics of the human Y chromosome palindromes, we analysed by high-coverage next-generation sequencing (>50×) a 30 kb palindrome in 157 samples, chosen to represent the most divergent evolutionary lineages of the MSY. In this analysis we overcame the problem of a non-unique mapping of the sequencing reads, and we performed an analysis of the sequencing depth. The availability of a reliable Y chromosome phylogeny (for the 157 samples), based on the analysis of 3.3 Mb of X-degenerate unique regions, allowed us to identify several GC events and a peculiar mutational pattern within arms. Finally, by mapping GC events across the Y phylogeny, we were able to calculate a precise Y-Y GC rate

Power budget and reconstruction algorithms for through the wall radar imaging systems

In this paper a through the wall radar imaging (TWRI) system based on a step frequency radar is presented. The radar equation is used for assessing the system power budget and two algorithms, namely the delay and sum (DAS) and the range migration (RM) are used for the scenario reconstruction. The achieved results evidence the strong dependence of the radar-re-ceived power on the wall losses. A frequency of 4 GHz seems to be the maximum allowable for practical TWRI systems. A scenario with obstacles placed in visibility of the radar and another with a wall between the radar and the obstacles have been realized. For the first scenario, the DAS algorithm provided better results with respect to RM but with longer processing times. In the second case, only the DAS algorithm was implemented that was able to cor-rectly locate the obstacles

A Multiple Input Single Output Radar for Through-the-Wall Radar Imaging

A step frequency Radar for through-the-wall radar imaging applications, based on a vector network analyzer (VNA) and on a Multiple Input Single Output (MISO) architecture, is presented. The system was calibrated by removing the errors due to the connection cables, to the time delay introduced by the antennas and by the power amplifier. Using the Radar, the position of metallic targets both in the absence and in the presence of a wall was accurately identified. The data acquired by the Radar were processed using 4 algorithms present in the literature and a new FT-MUSIC algorithm developed by the Authors. All the considered algorithms were able to accurately reconstruct the position of the investigated targets both in the absence and in the presence of a wall

Disclosing complex mutational dynamics at a Y chromosome palindrome evolving through intra- and inter-chromosomal gene conversion

The human MSY ampliconic region is mainly composed of large duplicated sequences that are organized in eight palindromes (termed P1-P8), and may undergo arm-to-arm gene conversion. Although the importance of these elements is widely recognized, their evolutionary dynamics are still nuanced. Here, we focused on the P8 palindrome, which shows a complex evolutionary history, being involved in intra- and inter-chromosomal gene conversion. To disclose its evolutionary complexity, we performed a high-depth (50×) targeted next-generation sequencing of this element in 157 subjects belonging to the most divergent lineages of the Y chromosome tree. We found a total of 72 polymorphic paralogous sequence variants that have been exploited to identify 41 Y-Y gene conversion events that occurred during recent human history. Through our analysis, we were able to categorize P8 arms into three portions, whose molecular diversity was modelled by different evolutionary forces. Notably, the outer region of the palindrome is not involved in any gene conversion event and evolves exclusively through the action of mutational pressure. The inner region is affected by Y-Y gene conversion occurring at a rate of 1.52 × 10-5 conversions/base/year, with no bias towards the retention of the ancestral state of the sequence. In this portion, GC-biased gene conversion is counterbalanced by a mutational bias towards AT bases. Finally, the middle region of the arms, in addition to intra-chromosomal gene conversion, is involved in X-to-Y gene conversion (at a rate of 6.013 × 10-8 conversions/base/year) thus being a major force in the evolution of the VCY/VCX gene family

Regional differences in the accumulation of SNPs on the male-specific portion of the human y chromosome replicate autosomal patterns: Implications for genetic dating

Factors affecting the rate and pattern of the mutational process are being identified for human autosomes, but the same relationships for the male specific portion of the Y chromosome (MSY) are not established.We considered 3,390 mutations occurring in 19 sequence bins identified by sequencing 1.5 Mb of the MSY fromeach of 104 present-day chromosomes. The occurrence ofmutations was not proportional to the amount of sequenced bases in each bin, with a 2-fold variation. The regression of the number ofmutations per unit sequence against a number of indicators of the genomic features of each bin, revealed the same fundamental patterns as in the autosomes. By considering the sequences of the same region from two precisely dated ancient specimens, we obtained a calibrated region-specific substitution rate of 0.716 × 10-9/site/year. Despite its lack of recombination and other peculiar features, the MSY then resembles the autosomes in displaying a marked regional heterogeneity of the mutation rate. An immediate implication is that a given figure for the substitution rate only makes sense if bound to a specific DNA region. By strictly applying this principle we obtained an unbiased estimate of the antiquity of lineages relevant to the genetic history of the human Y chromosome. In particular, the two deepest nodes of the tree highlight the survival, in Central-Western Africa, of lineages whose coalescence (291 ky, 95%C.I. 253-343) predates the emergence of anatomicallymodern features in the fossil record