Cultural factor in the geographic distribution of personal names: pseudogenetic analysis of first names used to estimate the cultural component of coefficients of relationship by isonymy

By applying to given names formulations for analyzing the genetics of surname distributions, under certain assumptions one can separate the genetic components from the cultural components of surname distributions. Geographic distributions of surnames regularly yield larger coefficients of relationship or kinship within local populations than between them: for instance, Ri = 75 x 10(-5) within a local area in England but the Ri of those villages with all of England and Wales is 42 x 10(-5). On the contrary, the first names in an English and Welsh sample give essentially the same pseudocoefficient (based on first names) within registration districts (Ri = 354 x 10(-5) as between districts (Ri = 370 x 10(-5). Thus the decrease with distance of the coefficients based on surnames can be ascribed to the genetic component according to the Malécot principle, assuming that the first names are chosen in the same way as the surnames originated and consequently that the cultural component of surname distributions is no more localized than the distribution of given names (in this sample not at all).     

Distance decay of similarity,effects of environmental noise and ecological heterogeneity among species in the spatio‐temporal dynamics of a dispersal‐limited community

The joint spatial and temporal fluctuations in community structure may be due to dispersal, variation in environmental conditions, ecological heterogeneity among species and demographic stochasticity. These factors are not mutually exclusive, and their relative contribution towards shaping species abundance distributions and in causing species fluctuations have been hard to disentangle. To better understand community dynamics when the exchange of individuals between localities is very low, we studied the dynamics of the freshwater zooplankton communities in 17 lakes located in independent catchment areas, sampled at end of summer from 2002 to 2008 in Norway. We analysed the joint spatial and temporal fluctuations in the community structure by fitting the two‐dimensional Poisson lognormal model under a two‐stage sampling scheme. We partitioned the variance of the distribution of log abundance for a random species at a random time and location into components of demographic stochasticity, ecological heterogeneity among species, and independent environmental noise components for the different species. Non‐neutral mechanisms such as ecological heterogeneity among species (20%) and spatiotemporal variation in the environment (75%) explained the majority of the variance in log abundances. Overdispersion relative to Poisson sampling and demographic stochasticity had a small contribution to the variance (5%). Among a set of environmental variables, lake acidity was the environmental variable that was most strongly related to decay of community similarity in space and time.     

Sampling for Regional Monitoring of Nematode Communities in Agricultural Soils

Regional assessment of nematode communities to monitor the condition or ecological health of agricultural soils requires sampling programs with measures of known reliability and the ability to detect differences over time. Numbers of fields sampled in a region, samples taken per field, and subsamples assayed per sample must be balanced with cost to provide the best sampling scheme. We used components of variance from statewide surveys in North Carolina (1992) and Nebraska (1993) to estimate number of (i) fields to be sampled; (ii) 20-core, composite soil samples to be obtained for each field; and (iii) subsamples to be assayed for each composite sample to detect a specified amount of change in index values within a geographic region. Variances for these three components were used to estimate the degree of reliability for five ecologically based indices (four measures of maturity and one of diversity) of nematode communities. Total variance for maturity and diversity indices, based upon communities of free-living nematodes, was greater in North Carolina than in Nebraska; the opposite was true for indices based strictly upon maturity of communities of plant-parasitic nematodes or of all nematodes in soil. Variability within samples was greater in North Carolina than in Nebraska, especially for maturity indices based only upon free-living nematodes. We identified two possible sampling strategies for a regional survey: Option 1, with two independent samples per field and a single subsample assayed per sample, which would provide a reliability ratio value ≥0.6 for most indices; and Option 2, with three independent samples per field and two subsamples assayed per sample, which would provide a reliability ratio value ≥0.7 for several indices. When cost was considered, Option 1 was the better strategy. Number of fields to be sampled within a region or state varied with the index chosen; with specific indices, however, a 10% change in mean index value could be detected with a sample of 50 to 100 fields.     

Inbreeding avoidance in an isolated indigenous Zapotec community in the valley of Oaxaca, southern Mexico

We analyzed inbreeding using surname isonymy in an indigenous genetic isolate. The subjects were residents of a rural Zapotec-speaking community in the valley of Oaxaca, southern Mexico. The community can be classified as a genetic isolate with an average gene flow of < or = 3% per generation. Surnames were collected for individuals in each household in pedigree form using the culturally traditional patronym-matronym naming. Estimation of inbreeding from surname isonymy is facilitated by the traditional patronym-matronym name assignment among indigenous Mexican populations. A total of 2,149 individuals had valid surname patronym-matronym pairings, including 484 deceased ancestors. Surname isonymy analysis methods were used to estimate total inbreeding and to segregate it into random and nonrandom components. The surname isonymy coefficient computed from 119 isonymous surname pairings (119/2,149) was 0.0554. The estimated inbreeding coefficient from surname isonymy was 0.0138 (0.0554/4). The random and nonrandom components of inbreeding were F(r) = 0.0221 and F(n) = -0.0091, respectively. The results suggest that consanguinity is culturally avoided. Nonrandom inbreeding decreased total inbreeding by about 41%. Total estimated inbreeding by surname isonymy was 0.0138, which is similar to inbreeding estimated from a sample of pedigrees, 0.01. Socially prescribed inbreeding avoidance substantially lowered total F through negative nonrandom inbreeding. Even in the situation of genetic isolation and small effective population size (N(e)), estimated inbreeding is lower than may have otherwise occurred if inbreeding were only random. However, among the poorest individuals, socially prescribed jural rules for inbreeding avoidance failed to operate. Thus the preponderance of inbreeding appears to occur among the poor, economically disadvantaged in the community.     

Variability in stream macroinvertebrates at multiple spatial scales

1. We intensively sampled 16 western Oregon streams to characterize: (1) the variability in macroinvertebrate assemblages at seven spatial scales; and (2) the change in taxon richness with increasing sampling effort. An analysis of variance (ANOVA) model calculated spatial variance components for taxon richness, total density, percent individuals of Ephemeroptera, Plecoptera and Trichoptera (EPT), percent dominance and Shannon diversity.
2. At the landscape level, ecoregion and among‐streams components dominated variance for most metrics, accounting for 43–72% of total variance. However, ecoregion accounted for very little variance in total density and 36% of the variance was attributable to differences between streams. For other metrics, variance components were more evenly divided between stream and ecoregion effects.
3. Within streams, approximately 70% of variance was associated with unstructured local spatial variation and not associated with habitat type or transect position. The remaining variance was typically split about evenly between habitat and transect. Sample position within a transect (left, centre or right) accounted for virtually none of the variance for any metric.
4. New taxa per stream increased rapidly with sampling effort with the first four to eight Surber samples (500–1000 individuals counted), then increased more gradually. After counting more than 50 samples, new taxa continued to be added in stream reaches that were 80 times as long as their mean wetted width. Thus taxon richness was highly dependent on sampling effort, and comparisons between sites or streams must be normalized for sampling effort.
5. Characterization of spatial variance structure is fundamental to designing sampling programmes where spatial comparisons range from local to regional scales. Differences in metric responses across spatial scales demonstrate the importance of designing sampling strategies and analyses capable of discerning differences at the scale of interest.     

On the Theory of Partially Inbreeding Finite Populations. I. Partial Selfing

Some stochastic theory is developed for monoecious populations of size N in which there are probabilities beta and 1 - beta of reproduction by selfing and by random mating. It is assumed that beta much greater than N-1. Expressions are derived for the inbreeding coefficient of one random individual and the coefficient of kinship of two random separate individuals at time t. The mean and between-lines variance of the fraction of copies of a locus that are identical in two random separate individuals in an equilibrium population are obtained under the assumption that there is an infinite number of possible alleles. It is found that the theory for random mating populations holds if the effective population number is Ne = N'/(1 + FIS), where FIS is the inbreeding coefficient at equilibrium when N is infinite and N' is the reciprocal of the probability that two gametes contributing to random separate adults come from the same parent. When there is a binomial distribution of successful gametes emanating from each adult, N' = N. An approximation to the probability that an allele A survives if it is originally present in one AA heterozygote is found to be 2(N'/N)(FISS1 + (1 - FIS)S2), where S1 and S2 are the selective advantages of AA and AA in comparison with AA. In the last section it is shown that if there is partial full sib mating and binomial offspring distributions Ne = N/(1 + 3FIS).     

Genetic kinship among an isolated Adi tribe of Arunachal Pradesh: isonymy in the Adi Panggi

Isolated tribes in remote areas are important for genetic studies, and one such little known subtribe of the Adi tribe, namely, the Adi Panggi (Pangi) of the Upper Siang District of Arunachal Pradesh, India, was studied for surname distribution to deduce the deviation from random mating and genetic kinship between villages. The estimates of homonymy (homozygosity) vary between villages; husbands show wider variation (0.009 to 0.23) than wives (0.005 to 0.054). The remote villages of Sumsing and Sibum and Geku Town show lower entropy among husbands' surnames than among Panggi wives. The highest equivalent surname number was found among Sibum husbands (9.9), Panggi wives (12.6), and Panggi and non-Panggi wives (13.5). The estimates of unbiased random isonymy among husbands and wives together show the smallest values in Sibum (0.05) and the highest values in Sumsing and Ramku (0.16). The random and nonrandom components of the inbreeding coefficient show avoidance of inbreeding among the Panggi villages (-0.012 to -0.27) except in Sibum (0.012). Genetic kinship between villages based on the Mij distance shows different clusters of villages among husbands and wives. Both the Panggi wives and the Panggi and non-Panggi wives show a similar pattern of clustering between villages. The wide homonymy variation between villages among the patrilocal Adi Panggi indicates differential genetic kinetics among husbands and wives, avoidance of inbreeding, and female-oriented differential gene flow with little effect on the overall intervillage genetic kinship.     

Missing the rarest: is the positive interspecific abundance–distribution relationship a truly general macroecological pattern?

Lepidopterists have long acknowledged that many uncommon butterfly species can be extremely abundant in suitable locations. If this is generally true, it contradicts the general macroecological pattern of the positive interspecific relationship between abundance and distribution, i.e. locally abundant species are often geographically more widespread than locally rare species. Indeed, a negative abundance–distribution relationship has been documented for butterflies in Finland. Here we show, using the Finnish butterflies as an example, that a positive abundance–distribution relationship results if the geographically restricted species are missed, as may be the case in studies based on random or restricted sampling protocols, or in studies that are conducted over small spatial scales. In our case, the abundance–distribution relationship becomes negative when approximately 70 per cent of the species are included. This observation suggests that the abundance–distribution relationship may in fact not be linear over the entire range of distributions. This intriguing possibility combined with some taxonomic biases in the literature may undermine the generalization that for a given taxonomic assemblage there is a positive interspecific relationship between local abundance and regional distribution.     

Surname analysis of the Corsican population reveals an agreement with geographical and linguistic structure

The surname is a cultural trait that is extremely useful for historical and linguistic studies and can effectively be used as a genetic marker. In many human populations the surname is inherited in the paternal lineage, and can therefore be considered a marker for the Y chromosome. In this study, surnames were recorded from the white pages of telephone directories in current use in Corsica in 1993. All surnames present in thirteen villages scattered over the whole island and covering the main historical regions were transcribed. Surname variability was found to be higher in coastal villages, and lower in more isolated communities. The isonymy detected among the thirteen villages allowed the calculation of kinship values, visualized in a tree showing two main clusters, one referring to the northern villages and one encompassing the villages of the south. The pattern reflects the administrative division of the island, with the exception of Vico, which belongs to the southern administrative region but is geographically close to the northern villages, and Ghisoni, which belongs to the northern district but is more similar to the village of Bastelica in the southern district. The data presented here show a structure in the surname distribution that is in substantial agreement with the geographical patterns. The kinship values are consistent with a moderated gene flow among villages producing a surname structure according to the geographic features of the territory.     

Familial segregation in the iron age community of Alfedena, Abruzzo, Italy, based on osteodental trait analysis

Numerous authors have studied human cemetery remains with an eye toward identifying different socially stratified ethnic or kinship groups within the same population. The interments of the protohistoric graveyard of Alfedena, Abruzzo, Italy, show recurrent organization in separate structures, suggesting to several involved archaeologists that these structures express family groups and/or differences in social function of the occupants. This has induced us to analyze the possible biological implications of specific models for kinship groups, lineages, or mating forms in graveyards. One hundred ninety-six metric and nonmetric skeletal and dental variables were collected. The analysis of metric features was performed by analysis of variance and by calculating divergences between each pair of individuals. The position parameters of the inter-and intragroup distance distributions were then compared by means of nonparametric tests. The nonmetric features were analyzed by contingency tables. The partition of intercircle variance is twice as frequently significant for males (20 variables) as for females (10). For metric variables in males, 20.9% displayed a probability level less than 5% for the null hypothesis of random distribution of individuals in the circles. Fewer (10.3%, but still more than expected at random) reached this level of significance for the females. In the male groups, 19% of nonmetric features showed significant frequency differences, but this was true in only 4.3% of the females.(ABSTRACT TRUNCATED AT 250 WORDS)     

Population structure in the Connecticut Valley: II. A comparison of multidimensional scaling solutions of migration matrices and isonymy

In a previous paper (Swedlund et al., 1984) we have described the population structure of the historical Connecticut River Valley of Massachusetts in terms of matrimonial migration matrices. Using procedures described by Morton (1973), Harpending and Jenkins (1974), Jorde (1980), and others the exchanges between subdivisions which make up the matrices are made column stochastic and analyzed to predict genetic kinship. Subsequently the kinship estimates within and between subdivisions can be interpreted as genetic covariance and compared to the actual geographic distances between the respective subdivisions using a principal components analysis. In the present paper we extend these results by applying nonmetric multidimensional scaling to the migration matrices, and to isonymy matrices based on the same communities. We demonstrate that the multidimensional scaling configurations of marital migration represent the actual geographic relationships between the communities quite effectively for this particular case study from historical Massachusetts. Moreover, we argue that while these migration data may provide good estimates of social and genetic exchange between the subdivisions, surname analysis may also be informative of processes not revealed in the migration matrices alone.     

Ecological drivers switch from bottom–up to top–down during model microbial community successions

Bottom–up selection has an important role in microbial community assembly but is unable to account for all observed variance. Other processes like top–down selection (e.g., predation) may be partially responsible for the unexplained variance. However, top–down processes and their interaction with bottom–up selective pressures often remain unexplored. We utilised an in situ marine biofilm model system to test the effects of bottom–up (i.e., substrate properties) and top–down (i.e., large predator exclusion via 100 µm mesh) selective pressures on community assembly over time (56 days). Prokaryotic and eukaryotic community compositions were monitored using 16 S and 18 S rRNA gene amplicon sequencing. Higher compositional variance was explained by growth substrate in early successional stages, but as biofilms mature, top–down predation becomes progressively more important. Wooden substrates promoted heterotrophic growth, whereas inert substrates’ (i.e., plastic, glass, tile) lack of degradable material selected for autotrophs. Early wood communities contained more mixotrophs and heterotrophs (e.g., the total abundance of Proteobacteria and Euglenozoa was 34% and 41% greater within wood compared to inert substrates). Inert substrates instead showed twice the autotrophic abundance (e.g., cyanobacteria and ochrophyta made up 37% and 10% more of the total abundance within inert substrates than in wood). Late native (non-enclosed) communities were mostly dominated by autotrophs across all substrates, whereas high heterotrophic abundance characterised enclosed communities. Late communities were primarily under top–down control, where large predators successively pruned heterotrophs. Integrating a top–down control increased explainable variance by 7–52%, leading to increased understanding of the underlying ecological processes guiding multitrophic community assembly and successional dynamics.Subject terms: Microbial ecology, Community ecology     

The variance of sample heterozygosity

The variance of sample heterozygosity, averaged over several loci, is studied in a variety of situations. The variance depends on the sampling implicit in the mating system as well as on that explicit in the loci scored and individuals sampled. There are also effects of allelic distributions over loci and of linkage or linkage disequilibrium between pairs of loci. Results are obtained for populations in drift and mutation balance, for infinite populations undergoing mixed self and random mating, and for finite monoecious populations with or without selfing. For unlinked loci in drift/mutation balance, variances appear to be lessened more by increasing the number of loci scored than by increasing the number of individuals sampled. For infinite populations under the mixed self and random mating system, however, the reverse is true. Methods for estimating the variance of sample heterozygosity are discussed, with attention being paid to unbalanced data where not all loci are scored in all individuals.     

Power of different sampling strategies to detect quantitative trait loci variance effects

Summary Many studies have shown that segregating quantitative trait loci (QTL) can be detected via linkage to genetic markers. Power to detect a QTL effect on the trait mean as a function of the number of individuals genotyped for the marker is increased by selectively genotyping individuals with extreme values for the quantitative trait. Computer simulations were employed to study the effect of various sampling strategies on the statistical power to detect QTL variance effects. If only individuals with extreme phenotypes for the quantitative trait are selected for genotyping, then power to detect a variance effect is less than by random sampling. If 0.2 of the total number of individuals genotyped are selected from the center of the distribution, then power to detect a variance effect is equal to that obtained with random selection. Power to detect a variance effect was maximum when 0.2 to 0.5 of the individuals selected for genotyping were selected from the tails of the distribution and the remainder from the center.     

Effect of Mating Structure on Variation in Linkage Disequilibrium

Measurement of linkage disequilibrium involves two sampling processes. First, there is the sampling of gametes in the population to form successive generations, and this generates disequilibrium dependent on the effective population size (N_e) and the mating structure. Second, there is sampling of a finite number (n) of individuals to estimate the population disequilibrium.——Two-locus descent measures are used to describe the mating system and are transformed to disequilibrium moments at the final sampling. Approximate eigenvectors for the transition matrix of descent measures are used to obtain formulae for the variance of the observed disequilibria as a function of N_e, mating structure, n, and linkage or recombination parameter.——The variance of disequilibrium is the same for monoecious populations with or without random selfing and for dioecious populations with random pairing for each progeny. With monogamy, the variance is slightly higher, the proportional difference being greater for unlinked loci.     

Regional Gray Matter Density Associated with Cognitive Reflectivity–Impulsivity: Evidence from Voxel-Based Morphometry

When faced with a problem or choice, humans can use two different strategies: “cognitive reflectivity,” which involves slow responses and fewer mistakes, or “cognitive impulsivity,” which comprises of quick responses and more mistakes. Different individuals use these two strategies differently. To our knowledge, no study has directly investigated the brain regions involved in reflectivity–impulsivity; therefore, this study focused on associations between these cognitive strategies and the gray matter structure of several brain regions. In order to accomplish this, we enrolled 776 healthy, right-handed individuals (432 men and 344 women; 20.7 ± 1.8 years) and used voxel-based morphometry with administration of a cognitive reflectivity–impulsivity questionnaire. We found that high cognitive reflectivity was associated with greater regional gray matter density in the ventral medial prefrontal cortex. Our finding suggests that this area plays an important role in defining an individual’s trait associated with reflectivity and impulsivity.     

Mapping quantitative trait loci using multiple families of line crosses.

To avoid a loss in statistical power as a result of homozygous individuals being selected as parents of a mapping population, one can use multiple families of line crosses for quantitative trait genetic linkage analysis. Two strategies of combining data are investigated: the fixed-model and the random-model strategies. The fixed-model approach estimates and tests the average effect of gene substitution for each parent, while the random-model approach treats each effect of gene substitution as a random variable and directly estimates and tests the variance of gene substitution. Extensive Monte Carlo simulations verify that the two strategies perform equally well, although the random model is preferable in combining data from a large number of families. Simulations also show that there may be an optimal sampling strategy (number of families vs. number of individuals per family) in which QTL mapping reaches its maximum power and minimum estimation error. Deviation from the optimal strategy reduces the efficiency of the method.     

Comparison of distance based density estimates for some arid rangeland vegetation

A method was required for determining the effect of management on extensive populations of trees and shrubs in central Australian rangelands. One useful indicator of change in these populations is the density of individuals, and there are several methods available based on distance measurement for density estimation. This study compared those procedures. Samples were drawn by computer from ground maps of actual plant distributions for Acacia aneura, Cassia nemophila and Atalaya hemiglauca and from a map generated at random. These samples were drawn to examine the properties of the nearest neighbour, point centred quarter, conditioned distance and compound T-square estimates of density. Samples were drawn by two methods: simple random sampling and semisystematic sampling. In general, there was a tendency for all estimators of density to underestimate the true density of naturally occurring populations with the compound T-square method (Byth 1982) being most robust. The compound T-square method was least biased but its variance increased for more aggregated spatial distributions. Estimates of density were not altered by the use of semisystematic sampling, when compared to simple random sampling. The spatial distributions examined in this study have not previously been studied as theoretical models. Acacia aneura and Cassia nemophila showed some aggregation of clusters, while the Atalaya hemiglauca showed a more extreme form of clustering due to its root suckering propagation.     

Dynamics of Correlated Genetic Systems. V. Rates of Decay of Linkage Disequilibria in Experimental Populations of DROSOPHILA MELANOGASTER

The dynamic behavior of four-locus gametic frequency distributions was studied in five replicate cage populations of Drosophila melanogaster for up to 50 generations. The joint frequency distributions were resolved into gene frequencies and various disequilibrium measures. In addition, F statistics for marginal single-locus genotypic frequency distributions were followed through time. The gene frequency, disequilibrium and F statistics were obtained for four chromosome 3 enzyme marker loci [isocitrate dehydrogenase (3–27.1), esterase-6 (3–36.8), phosphoglucomutase (3–43.4) and esterase-C (3–49.0)]. The initial structure of the experimental populations featured random mating proportions, and two complementary gametic types with respect to the marker loci, thus assuring complete pairwise linkage disequilibrium among the markers.——The experimental results indicate: (1) the between-replicate variance in gene frequency varied substantially among loci, with isocitrate dehydrogenase showing the greatest between-replicate variance, and esterase-C the least. (2) The F statistics initially were strongly negative but decayed to the neighborhood of zero for all marker loci except esterase-C. The rate at which the F statistics approached zero varied among the marker loci, indicating substantial differences in the distribution of selective effects along the chromosome. The centromeric region, marked by esterase-C, shows the strongest selective effects. (3) The rate of decay of linkage disequilibrium was much faster than expected for pairs of neutral loci, averaging 1.82 times the neutral rate over all replicates and pairs of loci. This acceleration, which was observed for all six pairwise combinations of loci, was interpreted as resulting from the interaction between selection and recombination. Our experimental results are consistent with many investigations of linkage disequilibrium in natural populations of Drosophila melanogaster that show little or no disequilibrium among enzyme loci. (4) A fortuitous contamination of two cages revealed an apparent regulatory interaction between the migrant and nonmigrant chromosomes at the esterase-C locus. The migrant chromosomes were very rapidly absorbed into the recipient populations, despite this interaction. This result suggests that the dynamics of migration in populations may be phenomenologically richer than anticipated by simple theory.