Nonmetric multidimensional scaling: A numerical method

Kruskal, Joseph B.

doi:10.1007/bf02289694

Cited by 4,092 publications

(1,953 citation statements)

References 6 publications

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“…43 A Slatkin's linearized genetic distance matrix 51 was used for a graphical representation by means of an NM-MDS. 52 Because Val di Scalve stood out as a clear outlier in the first NM-MDS plotting, relegating the other populations in a cloud that was very hard to disentangle, this sample was subsequently excluded from NM-MDS and AMOVA computations.…”

Section: Analysis Of Population Structurementioning

confidence: 99%

An evolutionary approach to the medical implications of the tumor necrosis factor receptor superfamily member 13B (TNFRSF13B) gene

et al. 2009

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Coding variants in tumor necrosis factor receptor superfamily member 13B (TNFRSF13B) have been implicated in common variable immunodeficiency (CVID), but the functional effects of such mutations in relation to the development of the disease have not been entirely established. To examine the potential contribution of TNFRSF13B variants to CVID, we have applied an evolutionary approach by sequencing its coding region in 451 individuals belonging to 26 worldwide populations, in addition to controls, patients with CVID and selective IgA deficiency (IgAD) from Italy. The low level of geographical structure for the observed genetic diversity and the several neutrality tests performed confirm the absence of recent population-specific selective pressures, suggesting that TNFRSF13B may be involved also in innate immune functions, rather than in adaptive immunity only. A slight excess of rare derived alleles was found in patients with CVID, and thus some of these variants may contribute to the disease, implying that CVID probably fits the rare variants rather than the common disease/common variant paradigm. This also confirms the previous suggestion that TNFRSF13B defects alone do not cause CVID and that such an extremely heterogeneous immunodeficiency might be more likely related to additional, still unknown environmental and genetic factors.

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Section: Analysis Of Population Structurementioning

confidence: 99%

An evolutionary approach to the medical implications of the tumor necrosis factor receptor superfamily member 13B (TNFRSF13B) gene

et al. 2009

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“…62 Analysis of population structure Genetic distances (F ST ) between populations were calculated assuming the Tamura-Nei model of nucleotide substitution. 63 The genetic distance matrix was graphically summarized by NM-MDS, 64 using the software STATISTICA. We used the AMOVA 32 to assess the apportionment of genetic variance between the following continental groups of populations: West Africa (Fulane, Igbo and Yoruba), East Africa (Hadza and Maasai), China, Europe (Russia and Northern Europe) and South America (Cayapa and Quechuas from Tayacaja and San Martín de Pangoa).…”

Section: Estimates Of Genetic Diversitymentioning

confidence: 99%

Divergent patterns of linkage disequilibrium and haplotype structure across global populations at the interleukin-13 (IL13) locus

Tarazona‐Santos

Tishkoff

2004

Genes Immun

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Interleukin-13 (IL-13) is a cytokine involved in Th2 immune response, which plays a role in susceptibility to infection by extracellular parasites as well as complex diseases of the immune system such as asthma and allergies. To determine the pattern of genetic diversity at the IL13 gene, we sequenced 3950 bp encompassing the IL13 gene and its promoter in 264 chromosomes from individuals originating from East and West Africa, Europe, China and South America. Thirty-one singlenucleotide polymorphisms (SNPs) arranged in 88 haplotypes were indentified, including the nonsynonymous substitution Arg130Gln in exon 4, which differs in frequency across ethnic groups. We show that genetic diversity and linkage disequilibrium (LD) are not evenly distributed across the gene and that sites in the 5 0 and 3 0 regions of the gene show strong differentiation among continental groups. We observe a divergent pattern of haplotype variation and LD across geographic regions and we identify a set of htSNPs that will be useful for functional genetic association studies of complex disease. We use several statistical tests to distinguish the effects of natural selection and demographic history on patterns of genetic diversity at the IL13 locus.

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“…Pairwise genetic distances were calculated using the Jaccard coefficient (Jaccard 1908), based on which the data were processed by UPGMA (unweighted pair group method with arithmetic mean) method. Multidimensional scaling (Kruskal 1964) was also carried out in the program NTSYS-pc.…”

Section: Statistical Processing Of the Resultsmentioning

confidence: 99%

Taxonomic rank of <i>Tanacetum boreale</i> Fisch. ex DC. (Asteraceae)

et al. 2017

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This article presents the results of population-genetic analysis in four populations of Tanacetum vulgare (typical tansy) from Southern Siberia on the basis of the Randomly Amplified DNA Fingerprints (RAF). We used RAF to find certain molecular-genetic differences between the typical tansy and the northern tansy. Since the present results did not show any clear differences between the typical tansy and the northern tansy at species level, we suggest that T. vulgare includes two subspecies: the typical T. vulgare subsp. vulgare and T. vulgare subsp. boreale.

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Nonmetric multidimensional scaling: A numerical method

Cited by 4,092 publications

References 6 publications

An evolutionary approach to the medical implications of the tumor necrosis factor receptor superfamily member 13B (TNFRSF13B) gene

An evolutionary approach to the medical implications of the tumor necrosis factor receptor superfamily member 13B (TNFRSF13B) gene

Divergent patterns of linkage disequilibrium and haplotype structure across global populations at the interleukin-13 (IL13) locus

Taxonomic rank of <i>Tanacetum boreale</i> Fisch. ex DC. (Asteraceae)

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