Ancestral Descent Research Articles

Genetic architecture and selection of Anhui autochthonous pig population revealed by whole genome resequencing.

The genetic resources among pigs in Anhui Province are diverse, but their value and potential have yet to be discovered. To illustrate the genetic diversity and population structure of the Anhui pigs population, we resequenced the genome of 150 pigs from six representative Anhui pigs populations and analyzed this data together with the sequencing data from 40 Asian wild boars and commercial pigs. Our results showed that Anhui pigs were divided into two distinct types based on ancestral descent: Wannan Spotted pig (WSP) and Wannan Black pig (WBP) origins from the same ancestor and the other four populations origins from another ancestor. We also identified several potential selective sweep regions associated with domestication characteristics among Anhui pigs, including reproduction-associated genes (CABS1, INSL6, MAP3K12, IGF1R, INSR, LIMK2, PATZ1, MAPK1), lipid- and meat-related genes (SNX19, MSTN, MC5R, PRKG1, CREBBP, ADCY9), and ear size genes (MSRB3 and SOX5). Therefore, these findings expand the catalogue and how these genetic differences among pigs and this newly generated data will be a valuable resource for future genetic studies and for improving genome-assisted breeding of pigs and other domesticated animals.

Review: Mass Murder in California’s Empty Quarter: A Tale of Tribal Treachery at the Cedarville Rancheria, by Ray A. March

Review: <i>Mass Murder in California’s Empty Quarter: A Tale of Tribal Treachery at the Cedarville Rancheria</i>, by Ray A. March

Cassava mosaic virus in Africa: Functional analysis of virus coat proteins based on evolutionary processes and protein structure

African cassava mosaic virus (ACMV) has been identified as a typical example of a pathogenic microorganism that constitutes a global menace to cassava's profitable production, especially in Africa, where the highest economic yield loss of 34 million tons usually is recorded annually. Functional analysis of virus coat proteins based on evolutionary processes and structure of ACMV isolates from fifteen African countries was conducted with Indian cassava mosaic virus and East African cassava mosaic Malawi virus as checks. The study revealed that ACMV coat proteins (CPs) belong to the nuclear export factor BR1 family in the Gemini-coat protein superfamily. Moreover, the phylogenetic analysis performed shows a very strong affinity amongst the African isolates within their geographical regions without evidence of evolutionary divergence amongst all the isolates. Multiple sequence alignment of the genes revealed a highly conserved domain and three motifs. Thirteen of the isolates from Africa share similar physicochemical properties and possess DNA-binding property. A three-dimensional homology model structure was built for ACMV CPs with Ramachandran plot values between 99 and 100%. The gene annotation analysis predicted most of the coat proteins associated with the virion and virus capsid, undertaking mainly organic compound and nucleic acids binding molecular functions and shuttling as the dominant biological process. Therefore, this study established that ACMV isolates have common ancestral descent. These findings form a strong basis that could be harnessed by applying molecular techniques for effective detection and management of ACMV isolates, causing substantial cassava losses recorded annually across several continents of the globe.

Multi-state design of flexible proteins predicts sequences optimal for conformational change.

Computational protein design of an ensemble of conformations for one protein-i.e., multi-state design-determines the side chain identity by optimizing the energetic contributions of that side chain in each of the backbone conformations. Sampling the resulting large sequence-structure search space limits the number of conformations and the size of proteins in multi-state design algorithms. Here, we demonstrated that the REstrained CONvergence (RECON) algorithm can simultaneously evaluate the sequence of large proteins that undergo substantial conformational changes. Simultaneous optimization of side chain conformations across all conformations increased sequence conservation when compared to single-state designs in all cases. More importantly, the sequence space sampled by RECON MSD resembled the evolutionary sequence space of flexible proteins, particularly when confined to predicting the mutational preferences of limited common ancestral descent, such as in the case of influenza type A hemagglutinin. Additionally, we found that sequence positions which require substantial changes in their local environment across an ensemble of conformations are more likely to be conserved. These increased conservation rates are better captured by RECON MSD over multiple conformations and thus multiple local residue environments during design. To quantify this rewiring of contacts at a certain position in sequence and structure, we introduced a new metric designated 'contact proximity deviation' that enumerates contact map changes. This measure allows mapping of global conformational changes into local side chain proximity adjustments, a property not captured by traditional global similarity metrics such as RMSD or local similarity metrics such as changes in φ and ψ angles.

At-home genetic testing in pediatrics.

This review discusses the state of at-home genetic testing, including both direct-to-consumer and consumer-directed genetic testing, for children. At-home genetic testing continues to increase in popularity and laboratories are starting to offer tests geared towards newborns and children. Available at-home genetic tests for children address ancestral descent, supplement newborn screening, or provide risks for childhood and adult-onset disorders as well as pharmacogenomic data. However, there are aspects of at-home testing that are unique to children that both providers and parents need to be aware of before considering this type of testing; these include issues related to motivations for testing; privacy concerns; result interpretation; ethical, legal and social implications; and impact on family relationships, among others. This review addresses the challenges associated with at-home genetic testing in children and provides guidance for pediatricians and other health care providers who field inquiries about this type of testing or who are presented with at-home genetic test results for interpretation.

Painted origins: inscribed landscape histories in the Fortaleza pictograph style during the Andean, late pre-Hispanic period

ABSTRACT The headwaters of the Fortaleza River, Ancash, Peru are an understudied area, archaeologically. Seventeenth-century Spanish Colonial accounts from the region describe a general moiety distinction between highland pastoralist and agricultural communities and mention named corporate ancestral descent groups (ayllu). Pierre Duviols’ analysis of these accounts identified that these moieties were actually mixed, bi-ethnic communities that originated around A.D. 1350. To test these observations and analysis, this study focuses on a large complex of rock art from the region referred to as Fortaleza pictograph style and which is defined by large panels that are found in association with water springs, tombs and agricultural fields. Regional survey and excavation results are paired with these accounts and Duviols’ analysis to place in time when ayllus deployed rock art to construct location-based histories and in doing so, controlled resources, primarily water and heritage in a time characterized by social strife and unreliable resources.

Māori kinship and power: Ngāi Tūhoe 1894–1912

The large Urewera National Park of New Zealand, recently returned to control of the Tuhoe (and other Urewera) Māori, was originally established (1896-1907) as the Urewera District Native Reserve under their virtual home-rule. Discovery of extensive marriage alliances between clusters of Tuhoe hapu 'ancestral descent groups' involved in the 1899-1903 investigation raises the relationship between kinship and political economic power in the context of New Zealand colonisation. Guided by Eric Wolf's exploration of the kin-ordered mode of mobilising social labour, a detailed ethnohistorical study of the establishment of the reserve is reviewed here in terms of Tuhoe leaders' exercise of power in relation to one another, as well as the colonial government. In order to consider Wolf's conclusion that especially in the context of colonisation such leaders are likely to break through the bounds of their kinship order, confrontations from 1900-1912 between several well-known Tuhoe leaders, an extensive marriage alliance, and three hapu are reviewed in some detail. It is hoped that an ethnohistory of this example of Tuhoe kinship and power at the turn of last century can complement the current resurgence of Tuhoe (and other Urewera) control over their original reserve.

Automated Facial Recognition of Computed Tomography-Derived Facial Images: Patient Privacy Implications.

The recognizability of facial images extracted from publically available medical scans raises patient privacy concerns. This study examined how accurately facial images extracted from computed tomography (CT) scans are objectively matched with corresponding photographs of the scanned individuals. The test subjects were 128 adult Americans ranging in age from 18 to 60years, representing both sexes and three self-identified population (ancestral descent) groups (African, European, and Hispanic). Using facial recognition software, the 2D images of the extracted facial models were compared for matches against five differently sized photo galleries. Depending on the scanning protocol and gallery size, in 6-61% of the cases, a correct life photo match for a CT-derived facial image was the top ranked image in the generated candidate lists, even when blind searching in excess of 100,000 images. In 31-91% of the cases, a correct match was located within the top 50 images. Few significant differences (p>0.05) in match rates were observed between the sexes or across the three age cohorts. Highly significant differences (p<0.01) were, however, observed across the three ancestral cohorts and between the two CT scanning protocols. Results suggest that the probability of a match between a facial image extracted from a medical scan and a photograph of the individual is moderately high. The facial image data inherent in commonly employed medical imaging modalities may need to consider a potentially identifiable form of "comparable" facial imagery and protected as such under patient privacy legislation.

ARE MAORI HAPU ‘HOUSES’? ARE WHAKAPAPA ‘STRATEGIC IMPROVISATIONS’? THE ETHNOHISTORICAL EVIDENCE FROM NGAI TUHOE

A recent exchange regarding the nature of Maori hapu has revived the old controversy whether or not ancestral descent groups can be organised on the basis of cognatic descent (through either or both parents in each generation). An innovative application of Levi-Strauss’s concept of a house society, and Bourdieu’s theory of practice, has challenged an answer to the old controversy, widely accepted since the 1970s, that hapu are entire descent categories narrowed to actively involved descent groups. The alternative view argues that Maori hapu were probably never based on such ambiguous grounds, but rather have developed since the 1880s as an ideology legitimating the solidarity of extended families (whanau), other kin, and non-kin closely associated with a meeting house and resourceful leadership able to extend hospitality. In defense of the earlier view that hapu are cognatic descent groups and categories, and probably have been at least since the 1840s, this essay reviews the recent exchange and examines the ethnohistorical evidence from one Maori iwi, Ngai Tuhoe.

Bio-Repository of DNA in stroke (BRAINS): A study protocol

BackgroundStroke is one of the commonest causes of mortality in the world and anticipated to be an increasing burden to the developing world. Stroke has a genetic basis and identifying those genes may not only help us define the mechanisms that cause stroke but also identify novel therapeutic targets. However, large scale highly phenotyped DNA repositories are required in order for this to be achieved.MethodsThe proposed Bio-Repository of DNA in Stroke (BRAINS) will recruit all subtypes of stroke as well as controls from two different continents, Europe and Asia. Subjects recruited from the UK will include stroke patients of European ancestry as well as British South Asians. Stroke subjects from South Asia will be recruited from India and Sri Lanka. South Asian cases will also have control subjects recruited.DiscussionWe describe a study protocol to establish a large and highly characterized stroke biobank in those of European and South Asian descent. With different ethnic populations being recruited, BRAINS has the ability to compare and contrast genetic risk factors between those of differing ancestral descent as well as those who migrate into different environments.

On the Construction Process of the Surname/Ancestral Seat Descent Groups in Korea as seen through Genealogies

The uniform application in understanding the characteristics of Korean surname/ ancestral seat descent groups of the current concept of ``clan`` and ``lineage`` when tracing descent from a common ancestor ignores their respective historical construction process. This paper highlights some misleading results of research based on such a uniform application and suggests that certain categories be used rather than one single concept to accommodate the highly particular and complicated construction process of Korean surname / ancestral descent groups.

Smoking cessation intervention among pregnant women in South Africa

The objective was to determine the practices and beliefs of disadvantaged women with high smoking rates, their perceptions of antenatal services and their preference for smoking cessation intervention materials. The readiness of smokers to quit, in terms of stages of change, was also determined. The study took place in public sector antenatal clinics situated in Cape Town, Kimberley, Port Elizabeth, Johannesburg and Pretoria that provide care to predominantly women of mixed ancestral descent. A cross-sectional survey was used. Data were collected via a self-administered questionnaire from pregnant women who were currently smoking, had quit smoking before or during pregnancy and who had never smoked. A total of 796 women were interviewed of which 365 (45.9%) were smokers, 117 (14.7%) were quitters and 314 (39.4%) were non-smokers. Being in the pre-contemplation stage was reported by 28%, 36% indicated that they thought about quitting, while 36% said that they were in the preparation stage. Of the smokers and quitters 9.3% had stopped in the last 6 months (action stage), and 15% had stopped for longer (maintenance phase). 86% of women reported satisfaction with midwives and more than 60% rated interactive intervention methods such as support groups and talks by women who had stopped smoking most favourably. Most women who smoked were contemplating or preparing to stop smoking. Intervention programmes should target these groups of women and midwives could be used to implement the interventions by facilitating support from women who had successfully quit.

To the End of the Earth: A History of the Crypto-Jews of New Mexico (review)

To the End of the Earth: A History of the Crypto-Jews of New by Stanley M. Hordes. New York: Columbia University Press, 2005. 348 pp. $39.50. According this publication, a substantial number of secret or crypto-Jews who fled the Inquisition were among the Catholic founders of today's New Mexican Hispano community. book's first two chapters reflect the author's doctoral research on the well documented settlement of Portuguese crypto-Jews in colonial Old But the balance of the book is a procrustean effort identify Old Mexico's indisputably Portuguese crypto-Jews as modern New Mexico's indisputably founding fathers. In this way Stanley M. Hordes attempts justify his own well documented history of misrepresenting the region's modern, and largely Protestant, folkways, as colonial and crypto-Jewish. Hordes' claims were disconfirmed in my article in Jewish Folklore and Ethnology Review in 1996 and thus remain noteworthy for their ongoing popularity, rather than their scholarly accuracy. To a significant extent, local Hispano acceptance reflects the traditional mode of asserting overvalued, white ancestral descent in the multiracial Spanish-Americas, where, as Raphael Patai wrote in his article The Jewish Indians of Mexico, Spanish [white] descent, even Jewish descent, means a step up on the social scale. At the same time, widespread Jewish acceptance seems reflect a beleaguered peoples' need believe itself indomitable, as evidenced by a miraculous survival. However, despite acceptance at the popular level, it is ultimately Hordes who must go to the end of the earth defend a thesis that scholarship can only refute. Not surprisingly, he does it the only way it can be done: by abandoning scholarly method and relying, instead, on serious violations of scholarship norms. For example, Hordes introduces me his readers as Folklorist Judith Neulander, who has dismissed any presence in New either historical or contemporary . (p. 221). He thus misrepresents my disconfirmation of 1996, as well as my doctoral dissertation, both of which are cited in the book, and both of which clearly state: have consciously avoided suggesting that a presence never existed in New Mexico, not mention insist only that the canon is no evidence of that presence [I keep] an open mind on the possibility of cultural variation, and that would include crypto-Judaism in New Mexico. My position could not be clearer. Yet, in every reference my work, Hordes makes no attempt provide better scholarship. Rather, as in the example above, he responds scholarly argument the only way he can: by voicing righteous indignation at irrational positions that I have never taken. As always, Hordes' primary research strategy is over-generalization of superficially related cultural items. In this new book he resurrects an ancient Roman gambling top (in global Hispanic use), which he earlier claimed was a variant of the Hanukkah dreydl. Long before he made this claim, however, it was refuted by scholars whose work he never consulted; the dreydl is a Yiddish toy that appeared much later, borrowed from a pagan tradition in England and Germany, which was never used by Iberian Jews. In response this criticism, Hordes has revised the claim, now citing the toy as crypto-Jewish in that it was (purportedly) used by Hispanos celebrate Hanukkah when they first learned of the Ashkenazi custom. For support, he cites a colleague who eagerly provides it (unless Hordes misrepresents him, as well) by defining bricolage incorrectly, sweeping it into the same category as cultural borrowing: Kunin believed the toy may well exemplify the anthropological concept of bricolage, or the borrowing by one culture of elements from others. …

To the End of the Earth: A History of the Crypto-Jews of New Mexico (review)

To the End of the Earth: A History of the Crypto-Jews of New Mexico. By Stanley M. Hordes. (New York: Columbia University Press. 2005. Pp. xxiv, 348. $39.50.) More than twenty years ago, historian Stanley Hordes announced to the press and media that a substantial number of secret- or crypto-Jews who fled the Spanish Inquisition were among the founders of today's New Mexican Hispano community. His doctoral work of 1980 had previously compiled and organized existing documentation of a tragicaEy ill-fated Portuguese cryptoJewish settlement in Old Mexico, from ca. 1500 to the mid-1600's. His book on New Mexico therefore has merit in its opening chapters, but only to the extent that he repeats his dissertation. It falls from grace in (1) conflation of America's indisputably Portuguese crypto-Jews with the indisputably Spanish founders of New Mexico, (2) egregious misrepresentation of work that disconfirms him, and (3) mislabeling of twentieth- century Adventist, Apostolic, and Messianic Protestant folkways (e.g., six-pointed stars on cemetery crosses, Saturday observance of the Sabbath, giving Old Testament names to children, etc.) as both colonial and crypto-Jewish. Hordes' historical violation of scholarship norms led to a first disconfirmation in 1996 (the article won First Prize for best publication by a graduate student from The American Folklore Society); the work was subsequently developed into a doctoral dissertation at The Folklore Institute at Indiana University, 2001. Hordes' pseudo-ethnographic claims have also been disconfirmed in the new edition of the Encyclopedia of American Folklife (in press for 2006), and most recently, in an article I was asked to write for Patterns of Prejudice (in press for 2006) concerning his pseudo-scientific use of disease as a Jewish ethnic marker, published as an appendix in this book. To grasp the extent to which the book distorts New Mexico's historical, cultural, and genetic heritage, it is important to note that claims of crypto-Jewish descent preceded Hordes in the region, surfacing circa 1975 when previous claims to descent from Spanish conquistadors were finally disconfirmed. Claims to a prestige lineage-whether Spanish, or crypto-Jewish-have liistoricaEy been used to assert an overvalued line of white ancestral descent throughout the multiracial Spanish Americas, a preferred phenotypical line of ancestry assumed in New Mexico for all conquistadors (and all Jews), but not for all Hispanos. …

Folk taxonomy, prejudice and the human genome: using disease as a Jewish ethnic marker

ABSTRACT When the Human Genome Project was completed, scientists discovered whole new populations that were at risk of heritable disorders. This revelation entails an obligation to be scientifically accurate and socially responsible in the biological classification, or labelling, of these populations. Neulander will define as unscientific ‘folk taxonomy’ all biological classification according to cultural commonalities: those traits and characteristics that—like religious affiliation—can only be acquired through learning, and are not biologically heritable. Noting the widespread popularity of sweeping cultural characteristics into biological classification—as in use of the term ‘Jewish’ for certain heritable diseases—she examines the social consequences of giving religious labels to genetic disorders in multiracial New Mexico, where disease-based claims of ‘secret’ or crypto-Jewish forebears are being used to assert an overvalued line of white ancestral descent, and where use of the term ‘Jewish’ to determine who is at risk of heritable diseases is generating, in turn, the use of heritable diseases to determine who is a Jew. The phenomenon will be examined in both folkloric and academic contexts, since locals who seek crypto-Jewish legitimacy thereby striate, into colour-coded levels of human valuation, what is otherwise a cohesive society, bringing their academic enablers into active, legitimating complicity. Neulander's essay seeks to help readers distinguish between folkloric and academic motivations and methods for discerning and describing human differences. Finally, she proposes a more valid and reliable means of classifying populations at risk of heritable disorders, the better to ensure results that are both scientifically accurate and socially responsible.