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.

New insights into the evolution of human Y chromosome palindromes through mutation and gene conversion.

About one-quarter of the euchromatic portion of the male-specific region of the human Y chromosome consists of large duplicated sequences that are organized in eight palindromes (termed P1-P8), which undergo arm-to arm gene conversion, a proposed mechanism for maintaining their sequence integrity. Although the relevance of gene conversion in the evolution of palindromic sequences has been profoundly recognized, the dynamic of this mechanism is still nuanced. To shed light into the evolution of these genomic elements, we performed a high-depth (50×) targeted next-generation sequencing of the palindrome P6 in 157 subjects belonging to the most divergent evolutionary lineages of the Y chromosome. We found 118 new paralogous sequence variants, which were placed into the context of a robust Y chromosome phylogeny based on 7240 SNPs of the X-degenerate region. We mapped along the phylogeny 80 gene conversion events that shaped the diversity of P6 arms during recent human history. In contrast to previous studies, we demonstrated that arm-to-arm gene conversion, which occurs at a rate of 6.01 × 10 -6 conversions/base/year, is not biased toward the retention of the ancestral state of sequences. We also found a significantly lower mutation rate of the arms (6.18 × 10-10 mutations/base/year) compared with the spacer (9.16 × 10-10 mutations/base/year), a finding that may explain the observed higher inter-species conservation of arms, without invoking any bias of conversion. Finally, by formally testing the mutation/conversion balance in P6, we found that the arms of this palindrome reached a steady-state equilibrium between mutation and gene conversion.

High incidence of AZF duplications in clan-structured Iranian populations detected through Y chromosome sequencing read depth analysis.

The ampliconic region of the human Y chromosome consists of large duplicated sequences that can undergo non-allelic homologous recombination (NAHR), resulting in structural rearrangements that may cause infertility, especially when they occur in the azoospermia factor b/c (AZFb/c) region. Although AZF duplications have long been neglected due to the technical limitations of STS-based studies that focused mainly on deletions, recent next generation sequencing (NGS) technologies provided evidence for their importance in fertility. In this study, a NGS read depth approach was used to detect AZFb/c rearrangements in 87 Iranians from different ethnic groups. The duplication frequency in Iran proved to be twice as high as in the "1000 Genomes" dataset. Interestingly, most duplications were found in patrilineal ethnic groups, possibly as a consequence of their lower male effective population size which can counteract negative selection. Moreover, we found a large 8.0 Mb duplication, resulting in a fourfold increase in the copy number of AZFc genes, which to our knowledge is the largest duplication ever reported in this region. Overall, our results suggest that it is important to consider not only AZF deletions but also duplications to investigate the causes of male infertility, especially in patrilineal clan-based populations.

The genomic echoes of the last Green Sahara on the Fulani and Sahelian people.

The population history of the Sahara/Sahelian belt is understudied, despite previous work highlighting complex dynamics.1,2,3,4,5,6,7 The Sahelian Fulani, i.e., the largest nomadic pastoral population in the world,8 represent an interesting case because they show a non-negligible proportion of an Eurasian genetic component, usually explained by recent admixture with northern Africans.1,2,5,6,7,9,10,11,12 Nevertheless, their origins are largely unknown, although several hypotheses have been proposed, including a possible link to ancient peoples settled in the Sahara during its last humid phase (Green Sahara, 12,000-5,000 years before present [BP]).13,14,15 To shed light about the Fulani ancient genetic roots, we produced 23 high-coverage (30×) whole genomes from Fulani individuals from 8 Sahelian countries, plus 17 samples from other African groups and 3 from Europeans as controls, for a total of 43 new whole genomes. These data have been compared with 814 published modern whole genomes2,16,17,18 and with relevant published ancient sequences (> 1,800 samples).19 These analyses showed some evidence that the non-sub-Saharan genetic ancestry component of the Fulani might have also been shaped by older events,1,5,6 possibly tracing the Fulani origins to unsampled ancient Green Saharan population(s). The joint analysis of modern and ancient samples allowed us to shed light on the genetic ancestry composition of such ancient Saharans, suggesting a similarity with Late Neolithic Moroccans and possibly pointing to a link with the spread of cattle herding. We also identified two different Fulani clusters whose admixture pattern may be informative about the historical Fulani movements and their later involvement in the western African empires.

Sequence Read Depth Analysis of a Monophyletic Cluster of Y Chromosomes Characterized by Structural Rearrangements in the AZFc Region Resulting in DYS448 Deletion and DYF387S1 Duplication.

The azoospermia factor c region (AZFc), located in the long arm of the human Y chromosome, is frequently involved in chromosome rearrangements, mainly due to non-allelic homologous recombination events that occur between the nearly identical sequences (amplicon) that comprises it. These rearrangements may have major phenotypic effects like spermatogenic failure or other pathologies linked to male infertility. Moreover, they may also be relevant in forensic genetics, since some of the Y chromosome short tandem repeats (Y-STRs) commonly used in forensic analysis are located in amplicons or in inter-amplicon sequences of the AZFc. In a previous study, we identified four phylogenetically related samples with a null allele at DYS448 and a tetrallelic pattern at DYF387S1, two Y-STRs located in the AZFc. Through NGS read depth analysis, we found that the unusual Y-STR pattern may be due to a 1.6 Mb deletion arising concurrently or after a 3.5 Mb duplication event. The observed large genomic rearrangement results in copy number reduction for the RBMY gene family as well as duplication of other AZFc genes. Based on the diversity of 16 additional Y-STRs, we estimated that the duplication/deletion event occurred at least twenty generations ago, suggesting that it has not been affected by negative selection.

Treatment Outcome of Posterior Composite Indirect Restorations: A Retrospective 20-Year Analysis of 525 Cases with a Mean Follow-up of 87 Months.

The purpose of this study was to evaluate the survival of 525 composite indirect restorations in premolars and molars after a follow-up of 20 years. For each patient, the following variables were recorded and analyzed: age, sex, smoking status, presence of plaque according to O'Leary index, and presence of bruxism. For each restoration, the following variables were collected: restoration class, tooth type (premolar or molar), and restoration material. Mean 20-year survival rate of composite restorations was 57%, ranging from 44% to 75%. The Kaplan-Meier method demonstrated a probability of survival at 10 years of 80% and 90%. Surviving restorations kept their clinical characteristics extremely well, as assessed on the basis of the United States Public Health Service criteria. The results of this study demonstrate the efficacy of indirect composite restorations, confirming their reliability as a posterior prosthetic clinical option.

Quantification of the amount of dental material removed by selective grinding in wax dentures with photogrammetric measurements.

BACKGROUND: The use of photogrammetry may be a new method to quantify the amount of artificial dental material removed from the surface of each teeth during the grind procedure (SG). SG is necessary in each denture to reach a correct occlusion. It consists in a refine action on the prosthesis teeth's surface using milling machine tools, aimed to remove the interferences (pre-contacts) between upper and lower teeth during chewing. This measure is achieved after a comparison between pre and post-grinding 3D models. This new application could be of interest for both dentists and dental technicians because it could be used to evaluate, with a accurate numerical description, the action applied on teeth surfaces during the grinding process. Furthermore, results of the analysis could have some value for the dental industry, since the use of photogrammetry can improve the process, reducing costs during the design of artificial teeth and eventually this method could be used as a teaching tool both for dental and "dental technician" high school students. The purpose of this work is to measure the thickness of the artificial enamel removed during grinding phases. Usually, the dental technician adjusts the dental plate on the mount of the patient following the traditional method, without a quantitative evaluation of the material removed. The photogrammetric method (PM) proposed here allows to measure the amount of material removed during the grinding process. This measure is achieved after a comparison between pre and post-grinding 3D models. METHODS: Under control of three teachers (experts of dentures performed according to the Gerber method) ten complete dentures arrangements (upper and inferior arches) performed by dental students at the Prosthodontic Department of the University of Parma, Italy were analyzed with PM before and after SG. RESULTS: The average thickness variation between the pre and post-grinding dentures is within the range of 0.1÷0.4 mm. For the upper arches, the mean value of the SG process is 223 µm while for the inferior arches is 240 µm. Results show that the most important grind process in all models appear in correspondence of cusps, with values up to 1660 µm. On the other hand, in correspondence of the fossae the results show a moderate grind action: the value is around 200-300 µm. Conversely to guidelines thought to students: cusps undergo a greater grinding process than fossae, consequently cusps should be revisioned at least on their technical and morphological aspects. The average thickness variation between the pre and post-grinding dentures is within the range of 0.1÷0.4 mm, this mean an equal value loss of vertical dimension. Furthermore, the knowledge of the gauge material removed during the SG could be useful for dental industries, giving important information, that could be considered for project and design of artificial teeth. CONCLUSIONS: The FM implemented in this article has given satisfactory preliminary results, showing good accuracy, low costs and high versatility. It is necessary to highlight that this is an experimental method and that the present analysis is a pilot study that needs further evaluation. Nevertheless results obtained could be of some value for medical companies, in order to improve the artificial teeth's design and project. Moreover, such a method may serve as educational tool for dental students.