Problems with synthetic maps remain: reply to Rendine et al.
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Chromosome Mapping↗
Biomedical subjects
B A Thomson
Publications and source records attributed to B A Thomson.
A problem with synthetic maps.
Synthetic maps of human gene frequencies, which are maps of principal component scores based on correlation of interpolated surfaces, have been popularized widely by L. Cavalli-Sforza, P. Menozzi, and A. Piazza. Such maps are used to make ethnohistorical inferences or to support various demographic or historical hypotheses. We show from first principles and by analyses of real and simulated data that synthetic maps are subject to large errors and that apparent geographic trends may be detected in spatially random data. We conclude that results featured as synthetic maps should be approached with considerable caution.
Chromosome Mapping↗
Spatial genetic structure of human populations in Japan.
We studied spatial patterns for 24 allele frequencies representing 15 systems (blood antigens, enzymes, serum proteins, color blindness, and cerumen) in Japan. The total number of samples over all systems and localities is 1125. We investigated patterns of genetic variation graphically as interpolated allele frequency surfaces, as one-dimensional and directional correlograms, and by testing for the direction of maximal genetic autocorrelation. We examined the allele frequency surfaces by various techniques of spatial autocorrelation analysis and found 13 allele frequency surfaces from 9 genetic systems exhibiting significant spatial patterns. Several surfaces have clinal patterns along the major axis of the Japanese archipelago; others tend toward a maximum or minimum in south-central Honshu. Yet other allele frequencies show long-distance differentiation or patchiness. We discovered seven areas of rapid genetic change by using the wombling method. These areas largely reflect maritime and montane barriers, and some are associated with dialectal boundaries in these populations. The observed patterns support the hybridization or dual structure hypothesis for the peopling of Japan.
Alleles↗
Dermatoglyphic variation in Europe.
We describe the geographic variation patterns of 236 dermatoglyphic variables (118 for each sex) for 74 samples in Europe. Using principal components analysis and rotating to simple structure, we simplified these patterns to the first 20 axes, representing 74.2% of covariation. We then used heterogeneity tests, interpolated surfaces, one-dimensional and directional correlograms, and distances between correlograms to analyze the factor scores of these 20 axes. We also ordinated the 74 localities. The data are remarkable for showing little spatial autocorrelation, despite significant heterogeneity among localities. Only three factor axes exhibit consistently significant correlograms, indicating that there are few spatial patterns in the original variables in Europe. Almost all correlations between pairs of variables occur within serially homologous character sets and are thus developmentally determined. There is some support for demic diffusion from the southeast in finger patterns and ridge counts. We compare these results to those of previous studies and note that Lapps and Icelanders are outliers with respect to both genetics and finger tip variables, whereas Tatars are outliers with respect to craniometrics and dermatoglyphics.
Analysis of Variance↗
Historical population movements in Europe influence genetic relationships in modern samples.
We have newly constructed an ethnohistorical database consisting of 3460 records of ethnic locations and movements in Europe since 2200 B.C. Using this database, we computed vectors of proportions that peoples speaking various language families contributed to the gene pools of 2216 1 degree x 1 degree land-based quadrats of Europe. From these vectors we computed ethnohistorical distances as arc distances between all pairs of quadrats. We used these distances as predictors of genetic distances, which we calculated independently from 26 genetic systems. We find significant partial correlations between ethnohistorical and genetic distances when geographic distance, a common causative factor, is held constant. Ethnohistorical distances explain a significant amount of the genetic variation observed in modern populations. These results are highly robust to simulated errors in and omissions from the ethnohistorical database. Randomization tests show that the historical sequence of the movements does not affect estimates of the ethnohistory-genetics correlation, but the geographic locations of movements do. We track the development of the ethnohistory-genetics correlation through time and show it to be gradual and cumulative over the past 4200 years.
Ethnology↗
Genetic relationships of European populations reflect their ethnohistorical affinities.
From 420 records of ethnic locations and movements since 2000 B.C., we computed vectors describing the proportions which peoples of the various European language families contributed to the gene pools within 85 land-based 5 x 5-degree quadrats in Europe. Using these language family vectors, we computed ethnohistorical affinities as arc distances between all pairs of the 85 quadrats. These affinities are significantly correlated with genetic distances based on 26 genetic systems, even when geographic distances, a common causative factor, are held constant. Thus, the ethnohistorical distances explain a significant amount of the genetic variation observed in modern populations. Randomizations of the records by chronology result in loss of significance for the observed partial correlation between genetics and ethnohistory, when geography is held constant. However, a randomization of records by location only results in reduced significance. Thus, while the historical sequence of the movements does not seem to matter in Europe, their geographic locations do. We discuss the implications of these findings.
Alleles↗
Origins of the Indo-Europeans: genetic evidence.
Two theories of the origins of the Indo-Europeans currently compete. M. Gimbutas believes that early Indo-Europeans entered southeastern Europe from the Pontic Steppes starting ca. 4500 B.C. and spread from there. C. Renfrew equates early Indo-Europeans with early farmers who entered southeastern Europe from Asia Minor ca. 7000 BC and spread through the continent. We tested genetic distance matrices for each of 25 systems in numerous Indo-European-speaking samples from Europe. To match each of these matrices, we created other distance matrices representing geography, language, time since origin of agriculture, Gimbutas' model, and Renfrew's model. The correlation between genetics and language is significant. Geography, when held constant, produces a markedly lower, yet still highly significant partial correlation between genetics and language, showing that more remains to be explained. However, none of the remaining three distances--time since origin of agriculture, Gimbutas' model, or Renfrew's model--reduces the partial correlation further. Thus, neither of the two theories appears able to explain the origin of the Indo-Europeans as gauged by the genetics-language correlation.
Blood Group Antigens↗
Ion-spray mass spectrometry of marine neurotoxins.
Ion-spray mass spectrometry was investigated for the analysis of three marine neurotoxins: domoic acid, saxitoxin and tetrodotoxin. All three compounds gave positive-ion spectra with abundant ions of protonated molecules and no significant fragmentation. Domoic acid gave a negative-ion spectrum with a strong [M-H]- ion. Tandem mass spectrometry provided useful fragment-ion spectra for all compounds. Detection limits for flow injection analyses with selected-ion monitoring were determined to be 30 pg for saxitoxin, 100 pg for domoic acid and 200 pg for tetrodotoxin. Combining liquid chromatography with ion-spray mass spectrometry allowed the determination of domoic acid and some of its isomers in toxic shellfish tissue extracts.
Kainic Acid↗
Genetic changes across language boundaries in Europe.
By means of three different methods we investigated whether 59 allele frequencies and ten cranial variables show increased change at 29 language-family boundaries in Europe. The quadrat-variance method compares variances of map quadrats crossed by language-family boundaries to variances of quadrats that are not crossed. The rate-of-change method examines the directional derivative of surfaces of the variables perpendicular to a language-family boundary and compares these derivatives to the same quantities obtained by randomly placing the language boundaries on the map of Europe. The difference method tests whether these variables differ more across language-family boundaries than across randomly placed boundaries. These special data-analytic techniques had to be developed to avoid the problem of spatial autocorrelation of both language and biological data. All three methods indicate increased genetic change at language-family boundaries. Clearer and more pronounced results are obtained by the first two methods than by the difference method. Thirteen language-family boundaries show significant gene frequency change by at least one of the methods. Changes are more marked in gene frequencies than in cranial variables. Different allele frequencies mark the increased change at different language boundaries. A model, based on the known history of each language-family boundary, was constructed to predict whether given boundaries should exhibit increased genetic change. The model is in good agreement with the observed results.
Alleles↗
Determination of drugs in biological samples by thin-layer chromatography-tandem mass spectrometry.
In this work thin-layer chromatography-tandem mass spectrometry (TLC-MS-MS) allowed detection and confirmation of caffeine and nicotine in human urine and of butorphanol, betamethasone, and clenbuterol in equine urine. In most cases of trace analysis of labile compounds the drugs could not be identified unless they were developed on a TLC plate, scraped from the plate and the TLC scrape eluted with a suitable organic solvent prior to MS-MS. Usually a sample prepared in this way still had several components in it, but was sufficiently cleaned up to allow collision-induced dissociation (CID) experiments to unequivocally identify the drug. In contrast, trace levels of labile drugs could not be identified by CID experiments either directly from the raw urine extracts or by thermally desorbing them from the TLC scrape.
Animals↗
Determination of sulfa drugs in biological fluids by liquid chromatography/mass spectrometry/mass spectrometry.
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Animals↗
Applications of a versatile technique for trace analysis: atmospheric pressure negative chemical ionization.
The ability to use ambient air as a carrier and reagent gas in an atmospheric pressure chemical ionization source allows instantaneous air analysis to be combined with hypersensitivity toward a wide variety of compounds. The TAGA (Trace Atmospheric Gas Analyser) is an instrument which is designed to use both positive and negative atmospheric pressure chemical ionization (APCI) for trace gas analysis; this paper describes several applications of negative APCI which demonstrates that the technique is not limited to environmental monitoring. Examples are described which suggest that the TAGA can be used for the detection of illicit drugs and explosives, and for the analysis of breath or skin emissions, as well as for air pollution measurements. The applications are not restricted by the use of ambient air as a reagent gas; addition to the air carrier of various gases allows specific reagent ions such as Cl- or Br- to be generated. Furthermore, in certain situations pure gas carriers can be used to provide even more flexibility in the ion chemistry, with a short term absorber-desorber system used to transfer the sample from the ambient air into the ion source region. The potential uses for APCI are expanding continuously as the understanding of the complex ion-molecule chemistry grows. This paper underlines the complementary relation between the development of new negative chemical ionization (NCI) techniques and practical applications using the TAGA system.
Air↗