Identifying nineteenth century genealogical links from genotypes

We have developed a likelihood method to identify moderately distant genealogical relationships from genomewide scan data. The aim is to compare the genotypes of many pairs of people and identify those pairs most likely to be related to one another. We have tested the algorithm using the genotypes of 170 Tasmanians with multiple sclerosis recruited into a haplotype association study. It is estimated from genealogical records that approximately 65% of Tasmania's current population of 470,000 are direct descendants of the 13,000 female founders living in this island state of Australia in the mid-nineteenth century. All cases and four to five relatives of each case have been genotyped with microsatellite markers at a genomewide average density of 4 cM. Previous genealogical research has identified 51 pairwise relationships linking 56 of the 170 cases. Testing the likelihood calculation on these known relative pairs, we have good power to identify relationships up to degree eight (e.g. third cousins once removed). Applying the algorithm to all other pairs of cases, we have identified a further 61 putative relative pairs, with an estimated false discovery rate of 10%. The power to identify genealogical links should increase when the new, denser sets of SNP markers are used. Except in populations where there is a searchable electronic database containing virtually all genealogical links in the past six generations, the algorithm should be a useful aid for genealogists working on gene-mapping projects, both linkage studies and association studies.     

Small tooth sizes in a nineteenth century South Carolina plantation slave series

Sub-Saharan African (and derived) populations typically exhibit larger mean tooth crown diameters than whites in spite of considerable population variability. We report on a 19th century series of American black slaves from a single cemetery near Charleston, South Carolina, that possessed notably smaller crown sizes. Analysis identifies a characteristic set of differences compared to caucasians, including retention of large maxillary lateral incisors and disproportionately large premolars and molars. Regression of principal components scores (derived from the mesiodistal diameters) on the sum of all diameters (used here as a measure of overall tooth mass) confirms a basic ethnic difference between black and white odontometrics: significantly more of the tooth mass is apportioned to the cheek teeth (premolars, molars) in blacks than whites. The difference (expressed as residuals from linear regression on tooth mass) holds for the several groups assessed here despite considerable intergroup variability in tooth sizes. Potential explanations for the notably small diameters of this plantation series are speculative, but may involve kin-based divergences and/or reflect the natural intergroup differences extant in the African slave sources.     

Birth spacing and infant mortality: evidence for eighteenth and nineteenth century German villages

Data from an historical population in which fertility control was minimal and modern health services were mostly unavailable are used to show that there appears to have been a strong association between previous birth interval length and infant mortality, especially when the previous child survived. Although only imperfect proxies for breast-feeding practices and other potentially confounding factors are available for this population, the results suggest that the association between previous interval length and infant mortality in this population is not solely, or primarily, a function of differences in breast-feeding behaviour or socioeconomic status. Other factors, e.g. maternal depletion or sibling competition, are more likely to explain the observed association.     

Essay review: Science and politics in the nineteenth century

Essay review: Science and politics in the nineteenth century     

Isolation and marriage patterns in four South Tyrolean villages (Italy) during the nineteenth century

No information is currently available on the marriage patterns of German-speaking communities of the South Tyrol area. The aim of this study is to investigate the reproductive isolation of four South Tyrolean mountain villages during the 19th century. Data about 3953 marriages were drawn from existing pedigrees and completed with data from the parish registers of the studied villages to calculate the following indicators: age at marriage, endogamy, inbreeding from dispensations and from isonymy and repeated pairs of surnames among couples. The results show high levels of endogamy (78-87%) and an elevated age at marriage in all the studied villages. The percentages of consanguineous marriages (10-33%) vary considerably but result overall in relatively low inbreeding values (alpha 0.0015-0.0036; Ft 0.0098-0.0138). Levels of endogamy are consistent with the geographic characteristics of the area, while inbreeding values are lower than those observed in previous studies on Alpine communities. This is due to a low frequency of marriages between close relatives, probably related to the peculiar demographic and cultural characteristics of the studied populations that differentiate them from neighbouring Italian-speaking villages.     

Dental caries in nineteenth century Upper Canada

This study examines the presence of dental caries in a large sample of adult skeletons from the 19th century cemetery of St. Thomas' Anglican Church in Belleville, Ontario. The cemetery was used from 1821 to 1874. Caries prevalence and frequencies of diseased and missing teeth were calculated both by observing summary statistics of individual rates and by the total sample of teeth. Postmortem tooth loss is low in this sample and antemortem tooth loss is highest in first mandibular molars, all other molars and then premolars. Age at death, but not sex, was found to be significantly related to the overall Caries Rate while both age and sex were significantly associated with the Diseased-Missing Index. The increase in diseased and missing teeth in older individuals is expected while the sex difference is not explained by simple dietary factors. When compared to reports on British and American samples, caries and antemortem tooth loss in the St. Thomas' sample is most similar to a pre-1850 British group and higher than American samples. Although there is undoubtedly a complex of factors contributing to caries prevalence in this sample, more data are required from large historic samples, particularly from the American northeast and late 19th century Britain, to have a clearer understanding of the influence of diet, cultural, and environmental factors affecting caries rates in historic populations. Am J Phys Anthropol 104:71–87, 1997. © 1997 Wiley-Liss, Inc.     

Selection within organisms in the nineteenth century: Wilhelm Roux's complex legacy

Selectionism, or the extension of darwinian chance/selection dynamics beyond the individual level, has a long history in biological thought. It has generated important theories in immunology or neurology, and turns out to be a convincing framework to account for the intrinsic stochastic nature of core events in cellular biology. When looking back at the intellectual origins of selectionism, the essay by the German embryologist Wilhelm Roux, Der Kampf der Theile im Organismus (The Struggle of the Parts in the Organism - 1881) might be one, if not the earliest reference after the darwinian revolution. It describes the individual as a multilevel structure, where each level results from a 'darwinian' struggle of its parts (molecules, cells, tissues, organs). But Roux's theory, far from being a simple extension of natural selection, has complex and even conflictual relationships with darwinism. This essay is worth rediscovering as a subtle historical testimony of the evolutionary and developmental life sciences debates of its time. Moreover, some of its theses may also enrich some current debates among evolutionary biologists over levels of selection, and among cellular and molecular biologists over the status of determinism in biology today.     

A test of the child replacement hypothesis: nineteenth century Massachusetts

Child mortality experiences may affect subsequent fertility of couples by exerting a physiological effect, influencing length of birth, interval, or a replacement effect, in which couples continue to procreate in an attempt to reach a desired number of surviving offspring. Where biological constraints are potentially important, however, it may be difficult to distinguish between purely physiological and purely behavioral components of the process regulating production. Natural spacing of births and onset of sterility may be affected by health and diet and prior childbearing and breastfeeding practices. Biological pressures can, in turn, be infuenced behaviorally both by social custom and individual choice. Studies of 126 families in 19th century Massachusetts show that reduction in infant mortality is not a prerequisite for onset of family limitation. Results for the study population did not exhibit a relationship between parity progression ratios and the experience of child mortality, consisten with the child replacement hypothesis. 1 factor involved may be the parent's expectations of more than the desired number of children because of imperfect contraceptive technology at the time. Preference for the sex of children also may weaken overall replacement effect, since the death of a child of "undesired" sex will not be replaced. The cohort age-specific fertility patterns indicate that a reduction in overall fertility level in the communities studied was parity-dependent and directed at stopping childbearing at some given range of family size. At any rate, parents are not passive participants in a natural regime of births and deaths. While child replacement may be present in some societies, it is relatively inefficient and perhaps infrequent.     

Phylogeny of South American Bufo (Anura: Bufonidae) inferred from combined evidence

Despite the considerable research that has focused on the evolutionary relationships and biogeography of the genus Bufo, an evolutionary synthesis of the entire group has not yet emerged. In the present study, almost 4 kb of DNA sequence data from mitochondrial (12S, tRNA^Val, and 16S) and nuclear (POMC; Rag-1) genes, and 83 characters from morphology were analysed to infer a phylogeny of South American toads. Phylogenies were reconstructed with parsimony and maximum likelihood and Bayesian model-based methods. The results of the analysis of morphological data support the hypothesis that within Bufo , some skull characters (e.g. frontoparietal width), correlated with the amount of cranial ossification, are prone to homoplasy. Unique and unreversed morphological synapomorphies are presented that can be used to diagnose recognized species groups of South American toads. The results of all phylogenetic analyses support the monophyly of most species groups of South American Bufo . In most DNA-only and combined analyses, the South American (minus the B. guttatus and part of the ' B. spinulosus ' groups), North American, Central American, and African lineages form generally well-supported clades: ((((((((South America) (North America + Central America)) Eurasia) Africa) Eurasia) South America) West Indies) South America). This result confirms and extends prior studies recovering South American Bufo as polyphyletic. The biogeographical results indicate that: (1) The origin of Bufo predates the fragmentation of Gondwana; (2) Central and North American species compose the sister group to a large, 'derived' clade of South American Bufo ; and (3) Eurasian species form the sister group to the New World clade.  © 2006 The Linnean Society of London, Zoological Journal of the Linnean Society , 2006, 146 , 407–452.     

Biological relationship between Central and South American Chibchan speaking populations: evidence from mtDNA

We examined mitochondrial DNA (mtDNA) haplogroup and haplotype diversity in 188 individuals from three Chibchan (Kogi, Arsario, and Ijka) populations and one Arawak (Wayuú) group from northeast Colombia to determine the biological relationship between lower Central American and northern South American Chibchan speakers. mtDNA haplogroups were obtained for all individuals and mtDNA HVS-I sequence data were obtained for 110 samples. Resulting sequence data were compared to 16 other Caribbean, South, and Central American populations using diversity measures, neutrality test statistics, sudden and spatial mismatch models, intermatch distributions, phylogenetic networks, and a multidimensional scaling plot. Our results demonstrate the existence of a shared maternal genetic structure between Central American Chibchan, Mayan populations and northern South American Chibchan-speakers. Additionally, these results suggest an expansion of Chibchan-speakers into South America associated with a shift in subsistence strategies because of changing ecological conditions that occurred in the region between 10,000-14,000 years before present.     

Estimating prehistoric American Indian population size for united states area: Implications of the nineteenth century population decline and nadir

Implications of a revised United States American Indian nadir population and the pattern of decline leading to it are examined. Substituting the new nadir for that used by Dobyns (1966) lowers by several million his estimates of Indian population for the United States (and Canada) area. These estimates then become more compatible with ones currently being suggested by other scholars. The nineteenth century decline leading to this nadir is found to be remarkably linear. Assuming linearity in decline from initial European contact through the eighteenth century, an aboriginal population estimate of 1,845,183 for the United States area may be extrapolated, along with estimates for intervening years. The nineteenth century decline is then graphed with the data extrapolated to 1492. The resulting pattern of population decline is quite different from the ones suggested by Mooney (1928) and Dobyns (1966).     

Concerted changes in tropical forest structure and dynamics: evidence from 50 South American long-term plots

Several widespread changes in the ecology of old-growth tropical forests have recently been documented for the late twentieth century, in particular an increase in stem turnover (pan-tropical), and an increase in above-ground biomass (neotropical). Whether these changes are synchronous and whether changes in growth are also occurring is not known. We analysed stand-level changes within 50 long-term monitoring plots from across South America spanning 1971-2002. We show that: (i) basal area (BA: sum of the cross-sectional areas of all trees in a plot) increased significantly over time (by 0.10 +/- 0.04 m2 ha(-1) yr(-1), mean +/- 95% CI); as did both (ii) stand-level BA growth rates (sum of the increments of BA of surviving trees and BA of new trees that recruited into a plot); and (iii) stand-level BA mortality rates (sum of the cross-sectional areas of all trees that died in a plot). Similar patterns were observed on a per-stem basis: (i) stem density (number of stems per hectare; 1 hectare is 10(4) m2) increased significantly over time (0.94 +/- 0.63 stems ha(-1) yr(-1)); as did both (ii) stem recruitment rates; and (iii) stem mortality rates. In relative terms, the pools of BA and stem density increased by 0.38 +/- 0.15% and 0.18 +/- 0.12% yr(-1), respectively. The fluxes into and out of these pools-stand-level BA growth, stand-level BA mortality, stem recruitment and stem mortality rates-increased, in relative terms, by an order of magnitude more. The gain terms (BA growth, stem recruitment) consistently exceeded the loss terms (BA loss, stem mortality) throughout the period, suggesting that whatever process is driving these changes was already acting before the plot network was established. Large long-term increases in stand-level BA growth and simultaneous increases in stand BA and stem density imply a continent-wide increase in resource availability which is increasing net primary productivity and altering forest dynamics. Continent-wide changes in incoming solar radiation, and increases in atmospheric concentrations of CO2 and air temperatures may have increased resource supply over recent decades, thus causing accelerated growth and increased dynamism across the world's largest tract of tropical forest.     

Sex determination from the occipital condyle: discriminant function analysis in an eighteenth and nineteenth century British sample

Fragmentary human remains compromised by different types of inhumation, or physical insults such as explosions, fires, and mutilations may frustrate the use of traditional morphognostic sex determination methods. The basicranium is protected by a large soft tissue mass comprising muscle, tendon, and ligaments. As such, the occipital region may prove useful for sex identification in cases of significantly fragmented remains. The aims of this paper are to (1) evaluate sexual dimorphism in British cranial bases by manually recorded unilateral and bilateral condylar length and width as well as intercondylar measurements and (2) develop discriminant functions for sex determination for this cranial sample. The crania selected for this study are part of the 18th-19th century documented skeletal collection of St. Bride's Church, Fleet Street, London. Adult human skulls (n = 146; male75/female71) were measured to derive statistical functions. Results indicated that expression of sexual dimorphism in the occipital condylar region within the St. Bride's population is demonstrable but low. Crossvalidated classification accuracy ranged between 69.2 and 76.7%, and sex bias ranged from 0.3 to 9.7%. Therefore, the use of discriminant functions derived from occipital condyles, especially in British skeletal populations, should only be considered in cases of fragmented cranial bases when no other morphognostic or morphometric method can be utilized for sex determination.