Inbreeding as measured by isonymy, pedigrees, and population size in Törbel, Switzerland.

Törbel provides an interesting test case for the study of the relationship between inbreeding measured by pedigrees and inbreeding measured by isonymy. At the start of this investigation, we were aware that isonymy could introduce biases into the calculation of the inbreeding coefficient in either direction. However, it was expected that in Switzerland, inbreeding from isonymy would be an overestimate due to patrilocal residence and polyphyletic names. One way of dealing with this problem [13] was not to be concerned with the absolute value of inbreeding but only in the difference between estimates. Any bias introduced in the estimate itself disappears in such comparisons, so that a trend of inbreeding can be ascertained correctly. However, it was considered equally important to subject several populations to both a complete pedigree analysis and an isonymic analysis to determine the relationship between estimates of inbreeding. Despite the fact that several authors (Swedlund [18], for example) warned users of isonymy to exercise caution, the careless application of isonymy still persists. In the present study, estimates of inbreeding from isonymy were brought into line with other methods based on pedigree analysis and population size. However, it was possible to do this only in Törbel where pedigree depth was extensive and relatively complete. Similar corrections are possible only when the distribution of mono- and polyphyletic names is known and when migration data are reliable. If the trouble is taken to make these corrections, the same time and effort might as well be spent in pedigree analysis (when fairly complete ascertainment is possible) to achieve the same end result.     

A study of contemporary levels and temporal trends in inbreeding in the Tangier Island, Virginia, population using pedigree data and isonymy

In this study we describe inbreeding in a large pedigree from Tangier Island, Virginia, in which we compare two commonly used methods to estimate inbreeding in humans: pedigree and isonymy (identical surnames of spouses). Genealogical data on 3,512 individuals dating back to 1722 were used. Using the pedigree method, we determined an average inbreeding coefficient (F) of 0.00873 for the community as a whole, and 0.018 for inbred individuals. Analysis of temporal trends showed that inbreeding began around 1800 and peaked at 0.0109 in 1824-1849 and 1875-1899. Thereafter, inbreeding steadily declined to 0.00565 in 1975-1997. Analysis of pedigree structure complexity over time showed that close consanguinity contributes to inbreeding in the earlier cohorts, and remote consanguinity accounts for much of the inbreeding in the later cohorts. The number of common ancestors increases over time, as does the number of paths connecting inbred individuals to these common ancestors. Inbreeding estimates based on the isonymy approach yielded a 2.2-fold higher value of F (0.01945) compared to the pedigree method. Total isonymy estimates over 25-year cohorts overestimated inbreeding values from pedigree data between 1. 5-8-fold. We speculate that the overestimation is probably due to the inability of our data to satisfy the method's assumption of monophyletic origin of each surname. In conclusion, inbreeding in the Tangier Island population is consistent with the isolated nature of its population, and temporal trends reflect patterns in emigration and a breakdown in isolation over time.     

Estimation of inbreeding by isonymy in Iberoamerican populations: an extension of the method of Crow and Mange

The method of isonymy for the estimation of inbreeding levels was extended to use the potentialities offered by the Iberoamerican surname system, in which a child inherits his surnames both from the father and the mother. Four possible types of isonymy were recognized between the family names of a husband-wife pair. It was found that, limited to simple consanguinity, the ratio between isonymy and the inbreeding coefficient of consanguineous individuals, starting from first cousins, is constant and equal to 16. Consanguinity levels were studied in four Venezuelan groups, Isla de Toas, Los Teques, Quibor, and Colonia Tovar, using genealogies, classical isonymy, and the extended method. It was found that, for Iberoamerican populations, the extended method is more precise than the classical method.     

Ancestral kinship and cancer in Lastovo Island, Croatia.

The aim of this study was to compute the average kinship coefficient of cancer cases in an extreme isolate (Lastovo Island, Croatia) and to compare it to the corresponding value for the island's unaffected population. Kinship estimates were obtained by Wright's path method (phi) based on pedigree reconstruction and Lasker's coefficient of relationship by isonymy (Ri) based on surname distribution. A total of 76 cancer cases were recorded on the island between 1971 and 1995. The unaffected control population of 1144 persons was obtained from the population census in 1971. The data on five ancestral generations were collected from parish registries preserved in the local church, and included 5484 persons born on the island between 1750 and 1970. Both Wright's path method and Lasker's isonymy method indicated significantly greater kinship of female cancer cases than of the unaffected population. Cancer cases with increased values of Ri among them and Ri among their ancestors included cancers of the ovary, colon, brain, breast, and prostate and leukemias. This study confirms the role of heredity and common ancestry in the development of cancer, providing a rough insight into their relative importance for specific cancer sites.     

Medico-genetic study of the population of Kostroma Province. VI. The parameters of isolation by distance in the populations of the Bui and Shar'ya Districts of Kostroma Province

A model of isolation by distance proposed by Malécot and developed by Morton is applied to the data on marriage distances collected in two regions of Kostroma Province. There is good agreement between the estimates of local inbreeding when using the isonymy method and the model of isolation by distance. Interpopulation kinship approaches 0 at the distance 700 km. The mean coefficient of kinship for parents in the families with autosomal-recessive pathology is 20 times higher than mean coefficient of kinship in the population.     

Testing isonymy with paternal and maternal lineages in the early Québec population: the impact of polyphyletism and demographic differentials

Isonymy is an ingenious and useful approach to studying kinship in human populations. However, it relies on assumptions that are difficult to verify. In this study, we provided a way to assess, in the early Québec population, the impact of factors such as polyphyletism, unbalanced sex-ratio among founders, and age differentials between spouses. All data were taken from the Population Register of Early Québec, which contains births, marriages, and deaths (>712,000) recorded in parish registers from the beginning of colonization (in 1608) to 1800. More specifically, using the 70,869 marriages recorded during that period, we compared kinship estimates given by genealogies, surnames, and paternal and maternal lineages. We also calculated a fifth coefficient of kinship by combining paternal and maternal lineage, thus providing a new way to test the isonymy method. The results show a good agreement between genealogical and isonymous estimates. However, this good correspondence is due to counterbalancing biases. Some of the implications of our results are discussed in the context of colonial America.     

Estimation of the upper limit of the mutation rate and mean heterozygous effect of deleterious mutations

Deng et al. have recently proposed that estimates of an upper limit to the rate of spontaneous mutations and their average heterozygous effect can be obtained from the mean and variance of a given fitness trait in naturally segregating populations, provided that allele frequencies are maintained at the balance between mutation and selection. Using simulations they show that this estimation method generally has little bias and is very robust to violations of the mutation-selection balance assumption. Here I show that the particular parameters and models used in these simulations generally reduce the amount of bias that can occur with this estimation method. In particular, the assumption of a large mutation rate in the simulations always implies a low bias of estimates. In addition, the specific model of overdominance used to check the violation of the mutation-selection balance assumption is such that there is not a dramatic decline in mean fitness from overdominant mutations, again implying a low bias of estimates. The assumption of lower mutation rates and/or other models of balancing selection may imply considerably larger biases of the estimates, making the reliability of the proposed method highly questionable.     

Genetic structure of the Saguenay, 1852-1911: evidence from migration and isonymy matrices

The Saguenay is a region in northeastern Québec populated in the second half of the 19th century through migration from other parts of Québec. The present-day population of nearly 300,000 is the result of both immigration and high rates of intrinsic growth. This population has been of interest to geneticists because of the high incidence of certain hereditary diseases, notably spastic ataxia, tyrosinemia, agenesis of the corpus callosum, vitamin D-dependent rickets, and myotonic dystrophy. Parent-offspring migration and isonymy matrices were used to estimate random kinship using the Malécot model for six 10-year time periods from 1852-1911. Comparisons between two estimates of kinship--one from parent-offspring migration matrices (phi) and the other from isonymy (R)--and geographic distance were made using both product-moment and Mantel correlation. Comparisons of within- and between-subdivision kinship were made using nonparametric and Mantel correlation. Within-subdivision kinship from the phi matrix was also compared with kinship estimated from marriage dispensations for endogamous marriages. The estimates of random kinship from the parent-offspring matrices showed a good fit with geography. However, isonymy did not correlate well with geographic distance; and phi and R showed no correlation until the last two time periods, and the diagonal of phi did not correlate with the marriage dispensations. Examination of scatterplots of phi vs. R suggests that nonrandom migration during the process of settlement formation is responsible for the lack of correlation. While movement across space seems to be highly dependent on distance, nonrandom selection of migrants means that between-subdivision estimates of kinship based on migration are not congruent with those obtained by other methods. On the whole, genetic differentiation seems to have been low due to the high levels of movement between subdivisions and immigration. The weak dependence of genetic structure on geographic distances in the present population is demonstrated by mapping the geographic distribution of cases of three recessively inherited diseases.     

Genetic structure of the Ards Peninsula,Northern Ireland: evidence from civil registers of marriage 1840-1911

This paper uses marital migration data transcribed from the Civil Registers of Marriage 1840-1911 to estimate kinship from migration matrices and isonymy in the Ards Peninsula, Northern Ireland. The distribution of religious denominations (Presbyterian, Episcopalian, and Roman Catholic) varies systematically throughout the region, with up to 77% Roman Catholic in the south and 81% Presbyterian in the north. Portavogie, a fishing village on the east coast, is exclusively Protestant, with a population 93% Presbyterian. Comparison of migration and isonymy with geographical distance by multidimensional scaling and the MATFIT procedure show Portavogie to be an outlier, more distantly related to other areas than its geographical position would predict. We suggest that this discrepancy is due to settlement history and occupational and religious isolation. Mantel tests show that marital migration is significantly related to geographical distance (rMG = 0.4257), as is the distribution of religious denominations (rRG = 0.5548) through settlement history. Migration is dependent on religion (rMR = 0.3674), and isonymy is dependent on migration (rIM= 0.2531) but not on geography or religion. With Portavogie omitted from the analysis, the dependence of migration on geography and on religion increases (rMG = 0.5583, rMR = 0.5646), as does the correlation between religion and geography (rRG = 0.7213). The dependence of isonymy on migration increases (rIM = 0.5103), and significant correlations between isonymy and religion (rIR = 0.4135) and isonymy and geography (rIG = 0.4660) appear. We argue that a full explanation of population structure requires geographical distance, settlement history, and the influence of religion and occupation to be taken into account.     

Fish stock assessment in lakes based on mass removal

The efficiency of mass removal of fishes can potentially be assessed using catch statistics collected during intensive fishing periods. The calculations are based on the general assumption that a decline in population size will produce a decline in catch per unit effort (cpue). When the removal is efficient it is possible to estimate the population size both at the beginning of the fishing period and after the removal.
Two examples are based on the winter seine net fishing of vendace ( Coregonus albula ) in Lake Pyhäjärvi, SW Finland in (1) 1983–1984 and (2) 1989–1990. The effects of the error in catch composition samples and random changes in probabilities of capture during the removal period on the final estimates of initial stock sizes are also examined.
The precision of the population estimates shown here was greatly influenced by the violation of the underlying assumption that the probability of capture is equal for all members of the target age group. In any case, particular attention should be paid to optimizing the sampling programme so that it will reveal the best information on the exploited stock with the resources in hand.     

The limitations of the isonymic method. From the model to an actual application on a computerized population register (Vallouise 1350–1899)

By means of a computerized population register integrating all the genealogies of a population of the French Alps from 1350 to the present time, we confront the theoretical concept of isonymy with observed reality. Born of the models of population genetics, isonymy allows an assessment of the average degree of kinship in a population as a result of unions of couples with the same surname. The simplicity of usage is only in appearance, since the process is upset by six hypotheses that are rarely verified. We are studying all the reservations one by one and only retain the suitable marriages as from 2,227, marriages appearing in the 19th century census. Originally, we have observed 168 couples bearing the same surname, yet only 39 actually correspond to the methodological criteria. Finally, many lessons are drawn from this study. This mountain example shows that where family kinship is concerned, there is always a remote, very remote component of this parameter. Despite our selection, assessment on the basis of isonymy turns out to be really much more important than the one established through genealogies. In the final analysis, before undertaking any research on isonymy, it is useful to carry out a precise study of the reference population, especially over a long period of time.     

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.     

Genetic structure of the Utah Mormons: isonymy analysis

Isonymy analysis is reported for a sample of 188,895 marriages extracted from the Utah Genealogical Database. Inbreeding rates estimated by isonymy are low, ranging from 0.005 for the earliest marriage cohort (1800-1809) to 0.0008 in the most recent cohort (1950-1959). The inbreeding values decrease considerably through time, but they are consistently higher than inbreeding values estimated from pedigrees. Several explanations are offered for this, including polyphyletism of surnames and the presence of Scandinavian patronyms in this population. Random isonymy between subdivisions is also compared with random kinship estimated from migration matrices. In terms of within-subdivision kinship, the two approaches yield similar results. However, the results are quite dissimilar for between-subdivision kinship. This reflects the recent and nonrandom settlement of Utah by different ethnic groups with different surname distributions. In later time periods, the correlations between the two types of kinship estimates increase, showing that migration patterns (which are strongly determined by geographic distance) exert an increasing influence on the distribution of surnames. Logistic regression is performed on a subset of marriages (n = 88,202), using isonymous vs. nonisonymous marriage as the dependent variable. The independent variables are year of marriage, geographic distance between husband's and wife's birthplaces, endogamous vs. exogamous marriage, and population sizes of husband's and wife's birthplaces. Year of marriage and geographic distance are shown to be significant independent predictors of isonymous marriage.     

A study of surnames in China through isonymy

The isonymy structure of 1.28 billion people registered in China's National Citizen Identity Information System was studied at the provincial, prefectural, and county administrative division levels. The isonymy was 0.026 for China as a whole. The average value of isonymy was 0.033 for the 30 provinces, 0.035 for the 334 prefectures, and 0.040 for the 2811 counties. The isonymy in China was much higher than in other countries. This finding may be partly explained by the low number of surnames in the Chinese language. Two regional features can be identified from the geographic distributions of isonymy. One feature is that the middle and lower reaches of the Yangtze River had the lowest values of isonymy at both the provincial and county levels. The second feature is that most counties with the highest values of isonymy were distributed in the provinces with high proportions of ethnic minorities. According to the dendrogram of surname distances, several clusters could be identified. Most provinces in a cluster were conterminous with one another. The one exception could be explained by demic migration called "braving the journey to the northeast of China." Isolation by distance could be detected because the correlation coefficients between Nei's distance and the geographic distances at the provincial, prefectural, and county levels were 0.64, 0.43, and 0.37, respectively. Human behaviors in Chinese history that may have caused these results have been discussed, including cultural origin, migration, residential patterns, and ethnic distribution.     

Marker selection for the transmission/disequilibrium test, in recently admixed populations.

Recent admixture between genetically differentiated populations can result in high levels of association between alleles at loci that are <=10 cM apart. The transmission/disequilibrium test (TDT) proposed by Spielman et al. (1993) can be a powerful test of linkage between disease and marker loci in the presence of association and therefore could be a useful test of linkage in admixed populations. The degree of association between alleles at two loci depends on the differences in allele frequencies, at the two loci, in the founding populations; therefore, the choice of marker is important. For a multiallelic marker, one strategy that may improve the power of the TDT is to group marker alleles within a locus, on the basis of information about the founding populations and the admixed population, thereby collapsing the marker into one with fewer alleles. We have examined the consequences of collapsing a microsatellite into a two-allele marker, when two founding populations are assumed for the admixed population, and have found that if there is random mating in the admixed population, then typically there is a collapsing for which the power of the TDT is greater than that for the original microsatellite marker. A method is presented for finding the optimal collapsing that has minimal dependence on the disease and that uses estimates either of marker allele frequencies in the two founding populations or of marker allele frequencies in the current, admixed population and in one of the founding populations. Furthermore, this optimal collapsing is not always the collapsing with the largest difference in allele frequencies in the founding populations. To demonstrate this strategy, we considered a recent data set, published previously, that provides frequency estimates for 30 microsatellites in 13 populations.     

A nondestructive method for estimating the age of Clapper Rail eggs

ABSTRACT.   Estimates of nest survival rate are often based on the assumption that the rate is constant during the nest cycle. Because violating this assumption can generate biased estimates, determining the age of a nest is important. For precocial marsh birds, including Clapper Rails ( Rallus longirostris ), current estimates of nest survival do not take this source of bias into account because a standardized, nondestructive method for aging eggs in not available. We developed a nondestructive flotation technique using known-age nests that can be used to estimate the projected hatch date of Clapper Rail eggs within 3 d of the actual hatch date. This precision is limited in part due to variance in the length of incubation between nests and the common occurrence of asynchronous hatching. However, for investigators assessing the fate of Clapper Rail nests, our technique provides an effective and nondestructive method for projecting the hatch date of Clapper Rail eggs, and will facilitate unbiased estimates of nest survival rates.     

Methods for the accurate estimation of confidence intervals on protein folding phi-values

Phi-values provide an important benchmark for the comparison of experimental protein folding studies to computer simulations and theories of the folding process. Despite the growing importance of phi measurements, however, formulas to quantify the precision with which phi is measured have seen little significant discussion. Moreover, a commonly employed method for the determination of standard errors on phi estimates assumes that estimates of the changes in free energy of the transition and folded states are independent. Here we demonstrate that this assumption is usually incorrect and that this typically leads to the underestimation of phi precision. We derive an analytical expression for the precision of phi estimates (assuming linear chevron behavior) that explicitly takes this dependence into account. We also describe an alternative method that implicitly corrects for the effect. By simulating experimental chevron data, we show that both methods accurately estimate phi confidence intervals. We also explore the effects of the commonly employed techniques of calculating phi from kinetics estimated at non-zero denaturant concentrations and via the assumption of parallel chevron arms. We find that these approaches can produce significantly different estimates for phi (again, even for truly linear chevron behavior), indicating that they are not equivalent, interchangeable measures of transition state structure. Lastly, we describe a Web-based implementation of the above algorithms for general use by the protein folding community.     

Population relationships by isonymy in frontier Pennsylvania.

Data from the 1800 US census were used to study relationships by isonymy among 7 civil subdivisions of Bedford County, Pennsylvania. Two analyses of the data were conducted. In the first analysis heads of household served as the unit of analysis. In the second analysis the total number of individuals in each household was used to correct for varying family sizes. All measures of internal differentiation were approximately doubled when the complete population numbers were used. The head-of-household analysis produced FST and RST values of 0.0012 and 0.0007, respectively; the complete population analysis yielded 0.0021 for FST and 0.0015 for RST. Interpopulation a priori kinship estimations were similar using both methods. Conditional kinship estimations varied more, with almost all values negative, but the head-of-household estimates were less negative. Multidimensional scaling of isonymy values coincided fairly well with actual geographic relationships, but a Mantel test revealed no significant relationship between geographic distances and isonymy, and isolation by distance values indicated a low relationship between the 2 measures. The population of the county was heterogeneous, with low kinship between its constituent communities. This appears to be a result of kin-structured long-distance migration rather than of local processes. The head-of-household values are more comparable with other studies and more representative of population relationships; complete population values exaggerate heterogeneity because of random fluctuations in household size.     

Note on estimates of the inbreeding coefficient through study of pedigrees and isonymous marriages

Crow and Mange (1965) developed a method to estimate the inbreeding coefficient (F) through an ingenious surname analysis. Such formulations assume a regularity of transmission of surnames, monophyletism, and random occurrence of consanguineous marriages. Accordingly, the ratio of isonymous partners to F of the offspring is equal to 4. Nevertheless, genealogy analyses show that the consanguineous marriages do not necessarily occur regularly. Therefore the isonymy analysis gives a misestimation of the inbreeding coefficient, depending on the prevailing form of nonrandomness. We suggest a small correction to the formulation in situations when pedigree information is available. The weighted mean of the ratio of isonymous partners to F of the known consanguineous marriages is suggested as a way to improve the formulas. The technique was applied to a northeastern Brazilian sample, and the results agree well with those of bioassays and therefore provide an apparently more realistic estimate of the inbreeding coefficient by isonymy.     

Estimation of the number of individuals founding colonized populations

A method for estimating the number of founding chromosomes in an isolated population is introduced. The method assumes that n/2 diploid individuals are sampled from a population and that alleles are identified at L unlinked loci. The population is assumed to have been founded T generations in the past by individuals carrying c chromosomes drawn randomly from a known source population, which has also been sampled. If c is small and the population grew rapidly after it was founded, accurate estimates of c can be obtained and those estimates are not sensitive to details of the history of population sizes. If c is larger or the population remained small after it was founded, then estimates of c depend on the history of population sizes. We test the performance of our method on simulated data and demonstrate its use on data from a rainbow trout (Oncorhynchus mykiss) population.