Search

Y haplogroups, defined by Y-SNPs, allow the reconstruction of the human Y chromosome genealogy. Recently, MPS based panels were introduced in the forensic genetics community for Y-SNP typing and identification of a broad range of haplogroups. The panels are based on an amplicon strategy and allow the detection of up to 15,600 Y-SNPs. The panels target up to 210,000 bps, which should be compared to the overall 8.9 Mbps comprising the unique regions of the non-recombining portion of the Y chromosome (NRY). We present an alternative approach of sequencing unique regions within the NRY using target enrichment probes and hybridization capture. A total of 359,954 probes were designed using the SureDesign software, representing 7.5 Mbps of the NRY. Library preparation and capture were performed using the Agilent SureSelect XT HS2 Target Enrichment method and sequencing was performed in a NovaSeq 6000 System. Besides individual barcodes, the method also included unique molecular barcodes for additional quality screening. The method was tested on admixed South Americans that carry a Y chromosome of haplogroup Q. We successfully identified novel variation that could potentially help refining haplogroup Q phylogeny.

Immigrants from diverse origins have arrived in Paraguay and produced important demographic changes in a territory initially inhabited by indigenous Guarani. Few studies have been performed to estimate the proportion of Native ancestry that is still preserved in Paraguay and the role of females and males in admixture processes. Therefore, 548 individuals from eastern Paraguay were genotyped for three marker sets: mtDNA, Y-SNPs and autosomal AIM-InDels. A genetic homogeneity was found between departments for each set of markers, supported by the demographic data collected, which showed that only 43% of the individuals have the same birthplace as their parents. The results show a sex-biased intermarriage, with higher maternal than paternal Native American ancestry. Within the native mtDNA lineages in Paraguay (87.2% of the total), most haplogroups have a broad distribution across the subcontinent, and only few are concentrated around the Paraná River basin. The frequency distribution of the European paternal lineages in Paraguay (92.2% of the total) showed a major contribution from the Iberian region. In addition to the remaining legacy of the colonial period, the joint analysis of the different types of markers included in this study revealed the impact of post-war migrations on the current genetic background of Paraguay.

Y haplogroups, defined by Y-SNPs, allow the reconstruction of the human Y chromosome genealogy, which is important for population, evolutionary and forensic genetics. In this study, Y-SNPs were typed and haplogroups inferred with the MPS Ion AmpliSeq™ HID Y-SNP Research Panel v1, as a high-throughput approach. Firstly, the performance of the panel was evaluated with different DNA input amounts, reagent volumes and cycle numbers. DNA-inputs from 0.5 to 1 ng generated the most balanced read depth. Combined with full reagent and 19 cycles, this offered the highest number of amplicons with a sequencing read depth of at least 20 reads. Secondly, the sub-haplogroups of 182 admixed South Americans and Greenlanders belonging to haplogroup Q were inferred and tested for potential improvement in resolution. Most samples were assigned to lineage Q-M3 with some samples assigned to lineages upstream (Q-M346, L56, L57; Q-L331, L53; Q-L54; Q-CTS11969, CTS11970) or parallel (Q-L330, L334; Q-Z780/M971) to Q-M3. Only one sample was assigned to a downstream lineage (Q-Z35615, Z35616). Most individuals of haplogroup Q with NAM ancestry could neither be distinguished from each other, nor from half of the Greenlandic samples. Typing additional, known SNPs within lineage Q-M3, Z19483 and SA05, increased the resolution of predicted haplogroups. The search for novel variants in the sequenced regions allowed the detection of 42 variants and the subdivision of lineage Q-M3 into new subclades. The variants found in six of these subclades were exclusive to certain South American countries. In light of the limited differentiation of haplogroup Q samples, the additional information on known or novel SNPs disclosed in this study when using MPS Ion AmpliSeq™ HID Y-SNP Research Panel v1 should be included in the Yleaf software, to increase the differentiation of lineage Q-M3.

A new multidimensional scheme consistent with the International Union of Geological Sciences (IUGS) is proposed for the classification of igneous rocks in terms of four magma types: ultrabasic, basic, intermediate, and acid. Our procedure is based on an extensive database of major element composition of a total of 33,868 relatively fresh rock samples having a multinormal distribution (initial database with 37,215 samples). Multinormally distributed database in terms of log-ratios of samples was ascertained by a new computer program DOMuDaF, in which the discordancy test was applied at the 99.9% confidence level. Isometric log-ratio (ilr) transformation was used to provide overall percent correct classification of 88.7%, 75.8%, 88.0%, and 80.9% for ultrabasic, basic, intermediate, and acid rocks, respectively. Given the known mathematical and uncertainty propagation properties, this transformation could be adopted for routine applications. The incorrect classification was mainly for the “neighbour” magma types, e.g., basic for ultrabasic and vice versa. Some of these misclassifications do not have any effect on multidimensional tectonic discrimination. For an efficient application of this multidimensional scheme, a new computer program MagClaMSys_ilr (MagClaMSys—Magma Classification Major-element based System) was written, which is available for on-line processing on http://tlaloc.ier.unam.mx/index.html . This classification scheme was tested from newly compiled data for relatively fresh Neogene igneous rocks and was found to be consistent with the conventional IUGS procedure. The new scheme was successfully applied to inter-laboratory data for three geochemical reference materials (basalts JB-1 and JB-1a, and andesite JA-3) from Japan and showed that the inferred magma types are consistent with the rock name (basic for basalts JB-1 and JB-1a and intermediate for andesite JA-3). The scheme was also successfully applied to five case studies of older Archaean to Mesozoic igneous rocks. Similar or more reliable results were obtained from existing tectonomagmatic discrimination diagrams when used in conjunction with the new computer program as compared to the IUGS scheme. The application to three case studies of igneous provenance of sedimentary rocks was demonstrated as a novel approach. Finally, we show that the new scheme is more robust for post-emplacement compositional changes than the conventional IUGS procedure.

A new multidimensional classification scheme consistent with the chemical classification of the International Union of Geological Sciences (IUGS) is proposed for the nomenclature of High-Mg altered rocks. Our procedure is based on an extensive database of major element (SiO2, TiO2, Al2O3, Fe2O3t, MnO, MgO, CaO, Na2O, K2O, and P2O5) compositions of a total of 33868 (920 High-Mg and 32948 “Common”) relatively fresh igneous rock samples. The database consisting of these multinormally distributed samples in terms of their isometric log-ratios was used to propose a set of 11 discriminant functions and 6 diagrams to facilitate High-Mg rock classification. The multinormality required by linear discriminant and canonical analysis was ascertained by a new computer program DOMuDaF. One multidimensional function can distinguish the High-Mg and Common igneous rocks with high percent success values of about 86.4% and 98.9%, respectively. Similarly, from 10 discriminant functions the High-Mg rocks can also be classified as one of the four rock types (komatiite, meimechite, picrite, and boninite), with high success values of about 88% to 100%. Satisfactory functioning of this new classification scheme was confirmed by seven independent tests. Five further case studies involving application to highly altered rocks illustrate the usefulness of our proposal. A computer program HMgClaMSys was written to efficiently apply the proposed classification scheme, which will be available for online processing of High-Mg igneous rock compositional data. Monte Carlo simulation modelling and mass-balance computations confirmed the robustness of our classification with respect to analytical errors and post-emplacement compositional changes. This article is protected by copyright. All rights reserved.

Before the arrival of Spanish settlers, the East region of Paraguay, was inhabited by Guarani people. After the Paraguayan war in 1870, which ended in loss of a high percentage of the male population, the migration to the country was encouraged. Immigration data indicate a high input of Eurasians to the territory. Also, since 1960s, a large number of Brazilians and Argentineans arrived in Paraguay. Samples from the eastern provinces of Paraguay were sequenced for the mtDNA control region and 88% presented native American haplogroups. A preliminary study on the same samples using AIMs indicates a high autosomal contribution from Europe and native America. The comparison of both type of markers showed that the European ancestry for autosomes is higher than expected when averaging mtDNA and the Y chromosome. This result supports recent admixture between Paraguayans and other populations probably already admixed, where the men contributed with high European ancestry.

In order to establish the best statistical procedure for estimating improved compositional data in geochemical reference materials for quality control purposes, we evaluated the test performance criterion (πD|C) and swamping (πswamp) and masking (πmask) effects of 30 conventional and 32 new discordancy tests for normal distributions from central tendency slippage δ = 2-10, number of contaminants E = 1-4, and sample sizes n = 10, 20, 30, 40, 60, and 80. Critical values or percentage points required for 44 test variants were generated through precise and accurate Monte Carlo simulations for sample sizes nmin(1)100. The recursive tests showed overall the highest performance with the lowest swamping and masking effects. This performance was followed by Grubbs and robust discordancy tests; however, both types of tests have significant swamping and masking effects. The Dixon tests showed by far the lowest performance with the highest masking effects. These results have implications for the statistical analysis of experimental data in most science and engineering fields. As a novel approach, we show the application of three conventional and two new recursive tests to an international geochemical reference material (Hawaiian basalt BHVO-1) and report new improved concentration data whose quality is superior to all literature compositions proposed for this standard. The elements with improved compositional data include all 10 major elements from SiO2 to P2O5, 14 rare earth elements from La to Lu, and 42 (out of 45) other trace elements. Furthermore, the importance of larger sample sizes inferred from the simulations is clearly documented in the higher quality of compositional data for BHVO-1.

This paper presents a novel approach to identify and geolocate nutrient deficiencies in oil-palm plantations using a mobile application. The process starts when the user captures an image of an oil-palm leaf with the integrated camera of an Android smart device. Then, the application processes and classifies the image into four categories corresponding to: a healthy palm, or a specimen with a deficit of Potassium (K), Magnesium (Mg), or Nitrogen (N). Finally, the application shows the corresponding predictions on the screen and it includes the current timestamp and GPS coordinate. However, if the smart device has an internet connection, the application also sends the processed data to Microsoft Azure for long-term storage and it enables the visualization of historic predictions through a web report built with Microsoft Power BI. The developed application allows producers to obtain in situ diagnosis of plant deficiencies in their crops, helping nutrient management plans and crop management policies. The proposed solution can be easily scaled to hundreds of devices for field deployments because each mobile application is configured as an Internet-of-Things device in the Azure Cloud.

This paper shows that the population studied in the most populated departments of Paraguay does not present significant population substructure among the different geographical locations sampled, allowing the use of these genetic frequencies for forensic genetics purposes in Paraguay. Furthermore, information on 22 aSTR presented in this study increases the resolution in database searching, it is useful for resolution of deficient paternity cases or paternity cases with inconsistencies, increasing both, the Power of Discrimination and the Power of Exclusion. Fil: Vullo, Carlos. Laboratorio de Inmunogenetica y Diagnostico Molecular; Argentina Fil: Rotondo, Martina. Laboratorio de Genética Forense; Argentina Fil: Daguerre, Natalia. Laboratorio de Inmunogenetica y Diagnostico Molecular; Argentina Fil: Quiroz, Alfredo. Hospital Regional, Encarnación, Paraguay; Paraguay Fil: Velásquez, Vanesa. Hospital Regional, Encarnación, Paraguay; Paraguay Fil: Machado, Patricia. Hospital Regional, Encarnación, Paraguay; Paraguay Fil: Serra, Horacio Marcelo. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Córdoba. Centro de Investigaciones en Bioquímica Clínica e Inmunología; Argentina Fil: Borosky, Alicia. Laboratorio de Inmunogenetica y Diagnostico Molecular; Argentina

"In this final paper of a series of four, using our well-tested simulation procedure we report new, precise, and accurate critical values or percentage points (with four to eight decimal places) of 15 discordancy tests with 33 test variants, and each with seven signifi cance levels = 0.30, 0.20, 0.10, 0.05, 0.02, 0.01, and 0.005, for normal samples of very large sizes n from 1,000 to 30,000, viz., 1,000(50)m 1,500(100)2,000(500)5,000(1,000)10,000(10,000)30,000, i.e., 1,000 (steps of 50) 1,500 (steps of 100) 2,000 (steps of 500) 5,000 (steps of 1,000) 10,000 (steps of 10,000) 30,000. The standard error of the mean is also reported explicitly and individually for each critical value. As a result, the applicability of these discordancy tests is now extended to practically all sample sizes (up to 30,000 observations or even greater). This final set of critical values for very large sample sizes would cover any present or future needs for the application of these discordancy tests in all fields of science and engineering. Because the critical values were simulated for only a few sample sizes between 1,000 and 30,000, six different regression models were evaluated for the interpolation and extrapolation purposes, and a combined natural logarithm-cubic model was shown to be the most appropriate. This is the first time in the literature that a log-transformation of the sample size n before a polynomial fi t is shown to perform better than the conventional linear to polynomial regressions hitherto used. We also use 1,402 unpublished datasets from quantitative proteomics to show that our multiple-test method works more effi ciently than the MAD_Z robust outlier method used for processing these data and to illustrate thus the usefulness of our final work on these lines."

In two earlier papers (Verma and Quiroz-Ruiz, 2006, Rev. Mex. Cienc. Geol., 23, 133-161, 302-319) precise critical values for normal univariate samples of sizes n up to 100 have been reported. However, for greater n, critical values are available only for a few tests: N1 for n up to 147, N4k2 for n up to 149, N6, N14 and N15 (for the latter three tests, critical values were reported for only n=200, 500, and 1000). This clearly demonstrates the need for proposing new critical values for n100 through an adequate statistical methodology. Therefore, modifications of our earlier simulation procedure as well as new, precise, and accurate critical values or percentage points (with four to eight decimal places; average standard error of the mean ~0.00000003–0.0039) of 15 discordancy tests with 33 test variants, and each with seven significance levels #945; = 0.30, 0.20, 0.10, 0.05, 0.02, 0.01, and 0.005, for normal samples of sizes n up to 1000, viz., nmin (1)100(5)200(10)500(20)1000, are reported. For the first time in the literature, the standard error of the mean is also reported explicitly and individually for each critical value. Similarly, a new methodology involving artificial neural network (ANN) was used, for the first time in published literature, to obtain interpolation equations for all 33 discordancy test variants and for each of the seven significance levels. Each equation was fitted using 76 simulated data for n from 100 to 1000 for a given test and significance level. Extremely small sums of squared residuals (~5.5 ×10-8 – 8.4 ×10-5; generally 10-5) in the ANN equations fitted for n=100 to 1,000 were obtained. As a result, the applicability of these discordancy tests is now extended up to 1000 observations of a particular parameter in a statistical sample. The new most precise and accurate critical values will result in more reliable applications of these discordancy tests than have been possible so far in various scientific and engineering fields, particularly for quality control in Earth Sciences. The multiple-test method with new critical values was shown to perform better than both the box-and-whisker plot and the “two standard deviation” methods used by some researchers, and is therefore the recommended procedure for handling experimental data

In this paper we report the simulation procedure along with new, precise, and accurate critical values or percentage points (with 4 decimal places; standard error of the mean #8804;0.0001) for six Dixon discordance tests with signifi cance levels #945; = 0.30, 0.20, 0.10, 0.05, 0.02, 0.01, 0.005 and for normal samples of sizes n up to 100. Prior to our work, critical values (with 3 decimal places) were available only for n up to 30, which limited the application of Dixon tests in many scientifi c and engineering fi elds. With these new tables of more precise and accurate critical values, the applicability of these discordance tests (N7 and N9-N13) is now extended to 100 observations of a particular variable in a statistical sample. We give examples of applications in many diverse fi elds of science and engineering including geosciences, which illustrate the advantage of the availability of these new critical values for a wider application of these six discordance tests. Statistically more reliable applications in science and engineering to a greater number of cases can now be achieved with our new tables than was possible earlier. Thus, we envision that these new critical values will result in wider applications of the Dixon tests in a variety of scientifi c and engineering fi elds such as agriculture, astronomy, biology, biomedicine, biotechnology, chemistry, environmental and pollution research, food science and technology, geochemistry, geochronology, isotope geology, meteorology, nuclear science, paleontology, petroleum research, quality assurance and assessment programs, soil science, structural geology, water research, and zoology.

In this paper, the modifi cations of the simulation procedure as well as new, precise, and accurate critical values or percentage points (for the majority of data with four decimal places; respective average standard error of the mean ~0.0001–0.0025) of nine discordancy tests, with 22 test variants, and each with seven signifi cance levels #945; = 0.30, 0.20, 0.10, 0.05, 0.02, 0.01, and 0.005, for normal samples of sizes n up to 100 are reported. Prior to our work, only less precise critical values were available for most of these tests, viz., with one (for n 20) and three decimal places (for greater n) for test N14; two decimal places for tests N2, N3–k=2,3,4, N6, and N15; and three decimal places for N1, N4–k=3,4, N5, and N8; but all of them with unknown errors. In fact, the critical values were available for n only up to 20 for test N2, up to 30 for test N8, and up to 50 for N4–k=1,3,4, whereas for most other tests, in spite of the availability for n up to 100 (or more), interpolations were required because tabulated values were not reported for all n in the range 3–100. Therefore, the applicability of these discordancy tests is now extended up to 100 observations of a particular parameter in a statistical sample, without any need of interpolations. The new more precise and accurate critical values will result in a more reliable application of these discordancy tests than has so far been possible. Thus, we envision that these new critical values will result in wider applications of these tests in a variety of scientifi c and engineering fi elds such as agriculture, astronomy, biology, biomedicine, biotechnology, chemistry, electronics, environmental and pollution research, food science and technology, geochemistry, geochronology, isotope geology, meteorology, nuclear science, paleontology, petroleum research, quality assurance and assessment programs, soil science, structural geology, water research, and zoology. The multiple-test method with new critical values proposed in this work was shown to perform better than the box-and-whisker plot method used by some researchers. Finally, the so-called “two standard deviation” method frequently used for processing inter-laboratory databases was shown to be statistically-erroneous, and should therefore be abandoned. Instead, the multiple-test method with 15 tests and 33 test variants, all of which now readily applicable to sample sizes up to 100, should be used. To process inter-laboratory databases, our present approach of multiple-test method is also shown to perform better than the “two standard deviation” method.