Multidimensional Scaling Plot Research Articles

Genetic position of Hungarian Grey among European cattle and identification of breed-specific markers

Hungarian Grey is an indigenous cattle breed that is one of the national symbols of Hungary. However, genetic description of the Hungarian Grey cattle has not yet been conducted based on whole-genome screening. Using the GeneSeek high-density Bovine SNP (single nucleotide polymorphism) 150 K BeadChip, we sampled the genome of 36 Hungarian Grey, 12 Maremmana, 13 Hungarian Fleckvieh and 5 Holstein-Friesian cattle for population studies and used data of 139 other cattle from an additional dataset created on European cattle breeds (Upadhyay et al.2017. Heredity 118, 169–176). The performance of a multidimensional scaling plot showed that Hungarian Grey clustered independently from other European cattle. The number and total length of runs of homozygosity (ROH) is similar or slightly below the value of other European cattle; FROH coefficients (proportion of the autosomal genome covered by ROH) are similar to Maremmana and Maronesa. The frequency of ROH does not show increased values as it can be noticed in Heck and Maltese. These results indicate that the Hungarian Grey cattle have been successfully maintained avoiding negative genetic effects, and reflect the uniqueness among European cattle. The identification of breed-specific loci has been aimed at differentiating Hungarian Grey (n = 136 in this case) from other cattle breeds (n = 169). Ten loci (−log10P > 5) were identified as markers capable for differentiation of Hungarian Grey. These markers are located on chromosomes 6, 14, 15, 16, 20 and 24.

Production, economic viability and risks associated with switching dairy cows from drylots to compost bedded pack systems

The use of compost bedded pack systems (CBS) has increased over the past 5 years in tropical countries, and studies associating production traits with economical outcomes of this system are warranted. Our objectives were to evaluate productive traits, economic outcomes and the risks of losses of dairy farms that switched from a drylot system (DLS) to a CBS and to compare these with similar farms that did not change their system. We collected data from 18 farms over 36 consecutive months (August 2014 to July 2017). All farms started the study as DLS, and six farms switched to CBS in the second year. The other 12 farms kept their DLS during the 36 months of evaluation. Annual technical and economic indexes per farm were collected and calculated. Additionally, a risk analysis was performed based on a 10-year historical series of milk prices. The results were analysed using a regression model including year and herd as categorical variables (fixed), system and herd size as quantitative variables (fixed), and system × herd as a random variable. Furthermore, a non-metric multidimensional scaling plot was used to evaluate producers’ profiles in each year. Milk fat, milk total solids, and somatic cell count did not change when farms switched from DLS to CBS, and averaged 3.80%, 12.04%, and 256 500 cells/ml, respectively. However, milk protein (%) decreased in CBS farms. The majority of milk production variables were not affected. Nevertheless, farms that switched to CBS increased milk production per cow by 13.3% compared with DLS farms. Total operation costs (296 076.83 $/year) were not affected by the system, and neither were the costs of concentrates, roughage, labour or medicines. Net margin per litre (0.09 $/l), operating profit (14.95%), assets per litre (398.68 $/l per day) and return on assets (10.27%) did not change when farms switched from DLS to CBS. Net margin ($/l and $/cow) and asset turnover rate increased in CBS farms. Risk analysis indicated that the risk was reduced by 38% in CBS farms. Furthermore, our analysis showed that producers who switched to CBS had similar technical and economic indexes in the first year before switching their system. In conclusion, this study demonstrates that CBS systems might be promising for producers in tropical countries who are looking for a more productive and less risky system. We did not observe improvements in animal health as previously reported in the literature.

A method for comparing perceptual distances and areas with multidimensional scaling

This paper presents a method for adding additional statistical comparisons to multidimensional scaling (MDS). The object of study in our work is perceptual distances between speech sound categories. Typically, MDS solutions do not receive inferential statistical treatment and their visualizations present average results across numerous participants. This is problematic because it ignores inter-participant variation. To account for this variance, we have devised a simple technique for adding statistical power to the traditional MDS solution so that the distances between objects and the areas occupied by groups of objects can be compared more reliably than visual inspection of an MDS plot. We provide a method for comparing distances between two objects and for comparing the area of three or more objects. This method can be paired with varying statistical analysis to suit the researcher's needs.•Adds statistical power to multidimensional scaling.•Compares distances between segments.•Compares dispersion of groups of objects in multidimensional space.

Forensic characteristics and genetic affinity analyses of Xinjiang Mongolian group using a novel six fluorescent dye-labeled typing system including 41 Y-STRs and 3 Y-InDels.

BackgroundY‐chromosomal genetic marker haplotypes of individuals can define the paternal kinship or genealogies to which they belong and further provide clues for forensic individual identifications. Studying the genetic structure of the Mongolian group will help to bring to light the Mongolian ethnic origin, and explicate the genetic affinities among the studied and compared populations. Some forensic scientists have studied the genetic background of the Mongolian group based on different molecular genetic markers. These studies were of very great reference significance for the Mongolian group genetic research, whereas the investigation of Y‐STR haplotype data in the Xinjiang Mongolian group is still insufficient.MethodsGenetic characteristics of 182 unrelated healthy male Mongolian individuals were revealed by 41 Y‐chromosomal short tandem repeat and 3 insertion/deletion molecular genetic markers. Furthermore, analyses of molecular variance programs, multi‐dimensional scaling plots, and phylogenetic tree reconstructions were operated to explore the genetic relationships of the Xinjiang Mongolian group with comparative 23 populations from China and 33 populations from worldwide nations.ResultsThe genetic diversity values ranged from 0.0641 (rs771783753) to 0.9502 (DYF387S1). A total of 165 distinct haplotypes were identified, of which 150 (90.91%) were unique. The discrimination capacity, match probability, and haplotype diversity of 44 loci were 0.9066, 0.0067, and 0.9988, respectively. Additionally, the Mongolian group had the most intimate relationship with Gansu Dongxiang (R ST = 0.0165), followed by HulunBuir Mongolian (R ST = 0.0187), Inner Mongolia Daur (R ST = 0.0202) as well as other three minority ethnic groups from the Xinjiang region (R ST < 0.05) in all compared Chinese populations, and clustered together with the majority of Asian populations in a worldwide scale.ConclusionsConsequently, the 44 loci could be well applied in forensic applications of the Mongolian group. The haplotypes available in here made new contributions to the existing population genetic information and would be of great value in population studies.

CyTOF workflow: differential discovery in high-throughput high-dimensional cytometry datasets

High-dimensional mass and flow cytometry (HDCyto) experiments have become a method of choice for high-throughput interrogation and characterization of cell populations. Here, we present an updated R-based pipeline for differential analyses of HDCyto data, largely based on Bioconductor packages. We computationally define cell populations using FlowSOM clustering, and facilitate an optional but reproducible strategy for manual merging of algorithm-generated clusters. Our workflow offers different analysis paths, including association of cell type abundance with a phenotype or changes in signalling markers within specific subpopulations, or differential analyses of aggregated signals. Importantly, the differential analyses we show are based on regression frameworks where the HDCyto data is the response; thus, we are able to model arbitrary experimental designs, such as those with batch effects, paired designs and so on. In particular, we apply generalized linear mixed models or linear mixed models to analyses of cell population abundance or cell-population-specific analyses of signaling markers, allowing overdispersion in cell count or aggregated signals across samples to be appropriately modeled. To support the formal statistical analyses, we encourage exploratory data analysis at every step, including quality control (e.g., multi-dimensional scaling plots), reporting of clustering results (dimensionality reduction, heatmaps with dendrograms) and differential analyses (e.g., plots of aggregated signals).

The impact of sample selection strategies on genetic diversity and representativeness in germplasm bank collections

BackgroundGermplasm banks maintain collections representing the most comprehensive catalogue of native genetic diversity available for crop improvement. Users of germplasm banks are interested in a fixed number of samples representing as broadly as possible the diversity present in the wider collection. A relevant question is whether it is necessary to develop completely independent germplasm samples or it is possible to select nested sets from a pre-defined core set panel not from the whole collection. We used data from 15,384, maize landraces stored in the CIMMYT germplasm bank to study the impact on 8 diversity criteria and the sample representativeness of: (1) two core selection strategies, a statistical sampling (DM), or a numerical maximization method (CH); (2) selecting samples of varying sizes; and (3) selecting samples of different sizes independently of each other or in a nested manner.ResultsSample sizes greater than 10% of the whole population size retained more than 75% of the polymorphic markers for all selection strategies and types of sample; lower sample sizes showed more variability (instability) among repetitions; the strongest effect of sample size was observed on the CH-independent combination. Independent and nested samples showed similar performance for all the criteria for the DM method, but there were differences between them for the CH method. The DM method achieved better approximations to the known values in the population than the CH method; 2-d multidimensional scaling plots of the collection and samples highlighted tendency of sample selection towards the extremes of diversity in the CH method, compared with sampling more representative of the overall genotypic distribution of diversity under the DM method.ConclusionsThe use of core subsets of size greater than or equal to 10% of the whole collection satisfied well the requirement of representativeness and diversity. Nested samples showed similar diversity and representativeness characteristics as independent samples offering a cost effective method of sample definition for germplasm banks. For most criteria assessed the DM method achieved better approximations to the known values in the whole population than the CH method, that is, it generated more statistically representative samples from collections.

Effect of nitrogen fertilisers on nitrous oxide emission, nitrifier and denitrifier abundance and bacterial diversity in closed ecological systems

In a 3-year microcosm study the nitrous oxide (N2O) emission from an agricultural soil amended with urea, ammonium sulphate or potassium nitrate were examined. Soil samples were taken every year to determine the soil physicochemical properties, the total abundance of bacteria, archaea, nitrifier and denitrifier communities and the changes in the structure and composition of the bacterial community. Gene abundance and biodiversity were estimated using quantitative PCR and pyrosequencing, respectively. The soils were watered weekly to reach 80% water filled pore space and varied from 80 to 62% during that time. N-fertilisation increased the abundance of bacteria and decreased that of archaea. Soils treated with ammonium or urea emitted more N2O than that amended with potassium nitrate and produced yearly increases in the abundance of nitrification genes. Also, the abundance of the denitrification genes gradually increased during the experimental period. N2O emission decreased on a yearly basis and so did the ratio of the genes involved in N2O production and reduction. A non-metric multidimensional scaling plot showed that N2O emission was positively related with the norB gene and negatively with the nosZ. The Shannon and Simpson diversity indices indicated that N-fertilisation reduced the number of operational taxonomic units (OTUs) and that the bacterial community became dominated by a small group of OTUs, respectively. N-fertilisation reduced the number of OTUs whose relative abundance was lower than 1%. We conclude that potassium nitrate reduces N2O emissions and increases the abundance of the N2O reducers. This work also shows that N-fertilisation decreases soil biodiversity and that its response depends on the type of the N-fertiliser.

Antonymous nature of freshwater phytoplankton in the tropical estuarine environments of Goa, southwest coast of India

Estuaries are the most dynamic marine ecosystems serving as potential spawning and nursery grounds for an array of marine fishes and their life stages. Producer community explicitly represented by phytoplankton form essential inertia to propagate the food chain, however on the contrary also could be detrimental due to blooming events. The present study envisages studying the distribution of green algae (Chlorophyceae) and blue–green algae (Cyanophyceae) in two tropical estuaries, namely Chapora and Sal in Goa along the west coast of India. Water samples were collected during July–December, 2016, comprising both monsoon and non-monsoon season. A total of twenty-five species of Chlorophyceae and three species of Cyanophyceae were recorded from these estuaries. Among the two, the Chlorophyceae group was found to be dominant and diverse. These two groups of phytoplankton were strongly influenced by the season in both the estuaries. The Multi-dimensional scaling (MDS) plots revealed salinity as one of the crucial parameters in the composition and distribution of these freshwater groups. Based on Redundancy analysis (RDA) plots, it was noted that, in addition to salinity, other physicochemical parameters (DO, pH, and nitrate concentration) could also affect the distribution of these groups. Two toxic bloom-forming genera (Microcystis and Oscillatoria) belonging to the Cyanophyceae group were reported. It is imperative that such events would play a role in the proliferation of these toxic species in the higher trophic levels.

Plant community recovery from intense deer grazing depends on reduction of graminoids and the time after exclosure installation in a semi-natural grassland.

Exclosures that exclude large herbivores are effective tools for the protection and restoration of grazed plant communities. However, previous studies have shown that the installation of an exclosure does not ensure plant community recovery. Our study aimed to determine the effects of the domination of unpalatable plants and the timing of exclosure installation on the plant community recovery process in montane grassland overgrazed by sika deer (Cervus nippon) in Japan. In this study we compared plant species composition and their cover with inside and outside exclosures installed at different times. Furthermore, we also compared them with those in 1981, when density of sika deer was very low. We used quadrats inside and outside fenced areas established in 2010 and 2011 to record both the cover and the height of species in each quadrat between 2011 and 2015. Plant cover, with the exception of graminoid species, increased in later years in all treatments. Non-metric multidimensional scaling (NMDS) plots showed significantly differentiated treatment trends. The species composition within the 2010 fenced area gradually shifted to greater similarity with the species composition reported in 1981. The plant community in the 2011 fenced area was slower to recover. Compositions of plant communities outside the fenced areas hardly changed from 2011 to 2015. Chao’s dissimilarity index decreased over time between the plant community surveyed between 2011 and 2015 and the past plant community in 1981 within the exclosures, and was higher in the 2011 fenced area than in the 2010 fenced area. In conclusion, we show that the reduction of graminoids and the time after exclosure installation were important for plant community recovery from deer grazing damage. A delay in exclosure installation of one year could result in a delay in plant community recovery of more than one year.

Population genetics of 25 Y-STR loci in Chinese Han population from Liaoning Province, Northeast China

In this study, we investigated the genetic characteristics of 25 Y-chromosomal short tandem repeat loci in 305 unrelated Chinese Han male individuals from Liaoning Province, using AmpFISTR® Yfiler® Plus amplification kit. A total of 293 different haplotypes were observed at the 25 Y-STR loci; among them, 281 were unique and 12 were occurred twice. The overall haplotype diversity was 0.9997 and the discrimination capacity was 0.9607. The gene diversity values ranged from 0.4525 (DYS391) to 0.9617 (DYS385). Population relationships between our data and other published populations were measured by Rst and visualized in two multi-dimensional scaling plots. The results showed that the 25 Y-STR loci in Liaoning Han population are valuable for forensic application and human genetics.

Chemical characterisation of potential pheromones from the shoulder gland of the Northern yellow-shouldered-bat, Sturnira parvidens (Phyllostomidae: Stenodermatinae).

Bats of the genus Sturnira (Family Phyllostomidae) are characterised by shoulder glands that are more developed in reproductively mature adult males. The glands produce a waxy secretion that accumulates on the fur around the gland, dyeing the fur a dark colour and giving off a pungent odour. These shoulder glands are thought to play a role in their reproductive behaviour. Using gas chromatography–mass spectrometry, we analysed solvent extracts of fur surrounding the shoulder gland in the northern-shouldered bat, Sturnira parvidens to (i) characterise the chemical composition of shoulder gland secretions for the first time, and (ii) look for differences in chemical composition among and between adult males, sub-adult/juvenile males and adult females. Fur solvent extracts were analysed as liquids and also further extracted using headspace solid-phase microextraction to identify volatile components in the odour itself. Odour fingerprint analysis using non-metric multidimensional scaling plots and multivariate analysis revealed clear and significant differences (P < 0.001) between adult males vs both juvenile males and adult females. The chemical components of the shoulder gland secretion included terpenes and phenolics, together with alcohols and esters, most likely derived from the frugivorous diet of the bat. Many of the compounds identified were found exclusively or in elevated quantities among adult (reproductive) males compared with adult females and non-reproductive (juvenile) males. This strongly suggests a specific role in male–female attraction although a function in male–male competition and/or species recognition is also possible.

Population background exploration and genetic distribution analysis of Pakistan Hazara via 23 autosomal STRs

Background: Short tandem repeats (STRs) have gained considerable attention in family search (Y-chromosomal STRs), complex paternity identification (X-chromosomal STRs), routine forensic personal identification (autosomal STRs) and population genetics.Aim: To explore the forensic characteristics of 23 autosomal STRs included in the Huaxia Platinum system in the South Pakistan Hazara population and investigate the genetic similarities and differences between Hazara and 54 worldwide reference populations.Subjects and methods: Variation of the 23 autosomal STRs included in the Huaxia Platinum system was first investigated and reported in a sample of 261 Quetta Hazara in Balochistan Province, Southwest Pakistan.Results: The combined power of discrimination is 0.999999999999999999999999999 and combined power of exclusion is 0.99999999989596 in Quetta Hazara. Comprehensive population comparisons between Hazara and another 13 Eurasian populations based on genotype data, as well as between Hazara and 54 worldwide populations based on the allele frequency distribution, were conducted. Multidimensional scaling plots, principal component analysis, and neighbour-joining phylogenetic trees consistently demonstrated that Pakistan Hazara harbours close affinities with neighbouring Turkic-speaking populations. Model-based genetic structure analysis further suggests that Quetta Hazara derives about half its ancestry directly from the East Asians.Conclusion: Twenty-five forensic-related markers included in the Huaxia Platinum system can be used for forensic practice in the Central Asia Hazara population. Quetta Hazara has a close genetic relationship with the Turkic-speaking populations of Uyghur and Kazakh. Further whole-genome sequencing of Hazara needs to be conducted to validate the observed genetic structure and reconstruct the fine-scale population history of Hazara.

Bacterial diversity in Korean temple kimchi fermentation.

Kimchi is manufactured using salted vegetables and various seasonings, including garlic, scallion, and jeotgal (fermented seafood). However, similar to vegan diets, Korean temple food does not contain animal products (meat- and seafood-free) and is restricted to five pungent herbs: garlic, scallion, leek, onions, and chives. In this study, we investigated the fermentation characteristics of 25 kimchi samples from traditional Korean temples or commercial sources using Illumina MiSeq sequencing. The initial pH of the kimchi samples ranged from 5.05 to 5.95 and the bacterial diversity-index showed a significantly high value in temple-style kimchi. Moreover, differences in microbial community were significantly reflected in kimchi types using non-metric multidimensional scaling plots and analysis of similarity. Additionally, the distribution patterns of the core bacterial genera differed according to kimchi type, especially during early phases of fermentation. These findings offer novel insights into the microbial ecology and quality characteristics of kimchi lacking vital ingredients, which are generally reported based on the origin of the microorganisms.

Genomic Insights of Dyadobacter tibetensis Y620-1 Isolated from Ice Core Reveal Genomic Features for Succession in Glacier Environment.

Glaciers have been recognized as biomes, dominated by microbial life. Many novel species have been isolated from glacier ecosystems, and their physiological features are well characterized. However, genomic features of bacteria isolated from the deep ice core are poorly understood. In this study, we performed a comparative genomic analysis to uncover the genomic features of strain Dyadobacter tibetensis Y620-1 isolated from a 59 m depth of the ice core drilled from a Tibetan Plateau glacier. Strain D. tibetensis Y620-1 had the smallest genome among the 12 cultured Dyadobacter strains, relatively low GC content, and was placed at the root position of the phylogenomic tree. The gene family based on a nonmetric multidimensional scaling (NMDS) plot revealed a clear separation of strain D. tibetensis Y620-1 from the reference strains. The genome of the deep ice core isolated strain contained the highest percentage of new genes. The definitive difference is that all genes required for the serine-glyoxylate cycle in one-carbon metabolism were only found in strain D. tibetensis Y620-1, but not in any of the reference strains. The placement of strain D. tibetensis Y620-1 in the root of the phylogenomic tree suggests that these new genes and functions are of ancient origin. All of these genomic features may contribute to the survival of D. tibetensis Y620-1 in the glacier.

Population genetics, diversity and forensic characteristics of Tai-Kadai-speaking Bouyei revealed by insertion/deletions markers.

China, inhabited by over 1.3 billion people and known for its genetic, cultural and linguistic diversity, is considered to be indispensable for understanding the association between language families and genetic diversity. In order to get a better understanding of the genetic diversity and forensic characteristics of Tai-Kadai-speaking populations in Southwest China, we genotyped 30 insertion/deletion (InDel) markers and amelogenin in 205 individuals from Tai-Kadai-speaking Bouyei people using the Qiagen Investigator DIPplex amplification kit. We carried out a comprehensive population genetic relationship investigation among 14,303 individuals from 84 worldwide populations based on allele frequency correlation and 4907 genotypes of 30 InDels from 36 populations distributed in all continental or major subregions and seven linguistic phyla in China. Forensic parameters observed show highly polymorphic and informative features for Asians, although the DIPplex kit was developed focusing on Europeans, and indicate that this amplification system is appropriate to forensic personal identification and parentage testing. Patterns of InDel variations revealed by principal components analysis, multidimensional scaling plots, phylogenetic relationship exploration, model-based clustering as well as four pairwise genetic distances (Fst, Nei, Cavalli-Sforza and Reynolds) demonstrate significant genetic differentiation at the continental scale and genetic uniformity in Asia except for Tibeto-Burman and Turkic-speaking populations. Additionally, Tai-Kadai speakers, including Bouyei, Zhuang and Dong, share more genetic ancestry components than with other language speakers, and in general they are genetically very similar to Hmong-Mien-speaking populations. The dataset of Bouyei people generated in the present study is valuable for forensic identification and parentage tests in China.

Host species and site of collection shape the microbiota of Rift Valley fever vectors in Kenya.

The composition and structure of microbial communities associated with mosquitoes remain poorly understood despite their important role in host biology and potential to be harnessed as novel strategies for mosquito-borne disease control. We employed MiSeq sequencing of the 16S rRNA gene amplicons to characterize the bacterial flora of field-collected populations of Aedes mcintoshi and Aedes ochraceus, the primary vectors of Rift Valley fever (RVF) virus in Kenya. Proteobacteria (53.5%), Firmicutes (22.0%) and Actinobacteria (10.0%) were the most abundant bacterial phyla accounting for 85.5% of the total sequences. Non-metric multi-dimensional scaling plots based on Bray-Curtis dissimilarities revealed a clear grouping of the samples by mosquito species, indicating that the two mosquito species harbored distinct microbial communities. Microbial diversity, richness and composition was strongly influenced by the site of mosquito collection and overall, Ae. ochraceus had significantly higher microbial diversity and richness than Ae. mcintoshi. Our findings suggest that host species and site of collection are important determinants of bacterial community composition and diversity in RVF virus vectors and these differences likely contribute to the spatio-temporal transmission dynamics of RVF virus.

Single Fragment or Bulk Soil DNA Metabarcoding: Which is Better for Characterizing Biological Taxa Found in Surface Soils for Sample Separation?

In forensic geology casework, sample size typically limits routine characterization of material using bulk approaches. To address this, DNA-based characterization of biological taxa has received attention, as the taxa present can be useful for sample-to-sample comparisons and source attribution. In our initial work, low biodiversity was captured when DNA barcodes were Sanger-sequenced from plant and insect fragments isolated from 10 forensic-type surface soils. Considering some forensic laboratories now have access to massively parallel sequencing platforms, we assessed whether biological taxa present in the same surface soils could be better characterized using DNA metabarcoding. To achieve this, plant and animal barcodes were amplified and sequenced on an Illumina® MiniSeq for three different DNA sample types (n = 50): individual fragments used in our initial study, and 250 and 100 mg of bulk soil (from the 10 sites used in the initial study). A total of 572 unique target barcode sequences passed quality filtering and were used in downstream statistical analyses: 54, 321, and 285 for individual fragments, 100 mg, and 250 mg bulk soil samples, respectively. Plant barcodes permitted some spatial separation of sample sites in non-metric multidimensional scaling plots; better separation was obtained for samples prepared from bulk soil. This study confirmed that bulk soil DNA metabarcoding is a better approach for characterizing biological taxa present in surface soils, which could supplement traditional geologic examinations.

Monitoring the Performance of Petrochemical Organizations in Saudi Arabia Using Data Envelopment Analysis

The petrochemical industry plays a crucial role in the economy of the Kingdom of Saudi Arabia. Therefore, the effectiveness and efficiency of this industry is of high importance. Data envelopment analysis (DEA) is found to be more acceptable in measuring the effectiveness of various industries when used in conjunction with non-parametric methods such as multiple regression, analytical hierarchy process (AHP), multidimensional scaling (MDS), and other multiple criteria decision making (MCDM) approaches. In this study, ten petrochemical companies in the Kingdom of Saudi Arabia are evaluated using Banker, Charnes and Cooper (BCC)/Charnes, Cooper, and Rhodes (CCR) models of DEA to compute the technical and super-efficiencies for ranking according to their relative performances. Data were collected from the Saudi Stock Exchange on key financial performance measures, five of which were chosen as inputs and five as outputs. Five DEA models were developed using different input–output combinations. The efficiency plots obtained from DEA were compared with the Euclidean distance scatter plot obtained from MDS. The dimensionality of MDS plots was derived from the DEA output. It was found that the two-dimensional positioning of the companies was congruent in both plots, thus validating the DEA results.

Population data of 23 Y chromosome STR loci for the five major human subpopulations of Ghana.

In this study, 268 samples for unrelated males belonging to the five major human subpopulation groups in Ghana (Akan, Ewe, Mole-Dagbon, Ga-Dangme and Guang) were genetically characterised for 23 Y chromosome short tandem repeat (STR) loci using the Powerplex® Y23 STR kit. A total of 263 complete haplotypes were recorded of which 258 were unique. The haplotype diversity, discriminating capacity and match probability for the pooled population data were 0.9998, 0.9627 and 0.0039, respectively. The pairwise genetic distance (RST) for the Ghanaian datasets and other reference populations deposited in the Y-STR Haplotype Reference Database (YHRD) were estimated and mapped using multidimensional scaling (MDS) plot. The Guang and Ewe were significantly different from the Akan, Mole-Dagbon and Ga-Dangme. However, the five Ghanaian datasets were all plotted close together with other African populations in the MDS data mapping.

Haplotype data for 17 Y-STR loci in the population of Himachal Pradesh, India.

We report here the data of Y chromosome haplotypes of 259 unrelated males from the population of Himachal Pradesh, India, using the Yfiler® multiplex kit. A total of 188 haplotypes were detected, out of which 148 were unique. Three samples showed bi-allelic pattern on locus DYS448. The observed genetic diversity and discrimination capacity were 0.996 and 0.73, respectively. In order to compare the genetic distance of the studied population with the published populations, multidimensional scaling (MDS) plot was constructed. The reported data is expected to be valuable for both forensic and population genetics.