Genetic Ancestors Research Articles

Analysis of the genetic diversity and genetic structure of Dermatophagoides farinae in different habitats using microsatellite markers

ABSTRACT The mite, Dermatophagoides farinae, is an allergen source that triggers allergy symptoms in humans. We studied how different habitats affect the genetic structure of D. farinae populations. We used 12 microsatellite loci to analyse the genetic structure of six D. farinae populations collected from four habitats: flour mill (FM), dormitory (DM), cotton mill (CM), and pillow (PL). The CM population had the highest genetic diversity (He = 0.641) while the FM population had less genetic diversity. AMOVA analysis showed 81% intrapopulation genetic variation and 19% interpopulation variation. The overall F ST value of the six populations was 0.18531, indicating significant population genetic differentiation. Significant genetic differentiation occurred between the FM population and the other three habitat populations. Bayesian clustering analysis showed that the FM population was divided into two clusters. UPGMA tree and PCoA data supported the above results and indicated that the D. farinae populations from CM, PL, and DM1 had similar genetic ancestors. It was speculated that D. farinae could spread through the cotton-pillow-dormitory route. This study showed that D. farinae may have undergone habitat-associated differentiation and provides measures for preventing the dispersal of D. farinae.

Counting the genetic ancestors from source populations in members of an admixed population.

In a genetically admixed population, admixed individuals possess genealogical and genetic ancestry from multiple source groups. Under a mechanistic model of admixture, we study the number of distinct ancestors from the source populations that the admixture represents. Combining a mechanistic admixture model with a recombination model that describes the probability that a genealogical ancestor is a genetic ancestor, for a member of a genetically admixed population, we count genetic ancestors from the source populations-those genealogical ancestors from the source populations who contribute to the genome of the modern admixed individual. We compare patterns in the numbers of genealogical and genetic ancestors across the generations. To illustrate the enumeration of genetic ancestors from source populations in an admixed group, we apply the model to the African-American population, extending recent results on the numbers of African and European genealogical ancestors that contribute to the pedigree of an African-American chosen at random, so that we also evaluate the numbers of African and European genetic ancestors who contribute to random African-American genomes. The model suggests that the autosomal genome of a random African-American born in the interval 1960-1965 contains genetic contributions from a mean of 162 African (standard deviation 47, interquartile range 127-192) and 32 European ancestors (standard deviation 14, interquartile range 21-43). The enumeration of genetic ancestors can potentially be performed in other diploid species in which admixture and recombination models can be specified.

Genetic Analysis of Birnirk Inuit from the Alaskan North Slope

Archaeological evidence indicates that Birnirk peoples (AD 650 – 1300) are the proposed genetic ancestors of the Thule Inuit (AD 950 – 1400) and are potentially an intermediary population between the Thule Inuit and earlier Old Bering Sea people (AD 1 – 1000). We sequenced the first hypervariable region of the mitochondrial DNA of 22 clearly associated Birnirk individuals from the Piġniq (Birnirk), Kugok, Kugusugaruk, and Nunavak sites on the North Slope of Alaska. Haplotypes A2a, A2a1, A2a3, A2b1, and D4b1a2a1a were identified in this population, demonstrating an expansion of Birnirk maternal genetic diversity. Maternal lineages from these individuals were evaluated with other past and contemporary Inuit populations from the Chukotka Peninsula to eastern Greenland. Our findings confirm Birnirk Inuit as probable maternal ancestors to Thule Inuit and may be among the first peoples possessing these lineages to have moved into the western North American Arctic from the Bering Strait region.

Genetic markers of domestication (some features of interpretation of laboratory data of paleogenetic researches)

The paper reviews the findings of two research groups, published in the journal Nature, that focus on the genetic aspects of horses domestication in the Bronze Age. Creating coherence and overcoming the contradictions between the data of paleogenetics and archeology through meta-description, which is based on the prevalence of selection, turns into the some controversial conclusions, including: extrapolation caused by the transfer of anthropomorphic characteristics to the physiological characteristics of the horse and the reduction of actors of social processes to genetic markers. In the context of articles on medical genetics and sociology of science, it is proposed to overcome controversies through a change in the optics of analysis of genetic data in the problem of domestication: rejection of the meta-description of the researching phenomena and the actualization of the logic of meeting social needs and mutational variability preceding domestication. In addition, the paper deals with the problem of interpreting the genetic data of horse domestication only as a hypothesis. The problem is that there is a significant chronological gap of 500-700 years between genetic ancestors and genuine domestic horses (Dom-2). This period includes such significant archaeological cultures as Abashevskaya, post-Poltavka Volga-Ural and others.

ВИТОКИ УКРАЇНСЬКОГО ТА ЄВРОПЕЙСЬКОГО АРХЕТИПІВ У КОНТЕКСТІ НООАНТРОПОЛОГІЇ

The author integrates new achievements of archeometry, paleogenetics and other sciences of the XXI century by the term "nooanthropology". The reasons for the European division into East and West are considered.. The facts about the temporal and territorial characteristics of the beginning of the transition from cannibalism to prahumanism are used. Undoubted evidence of this Neolithic progress in the range of 15-7 thousand years ago in Anatolia is given. The leaders of the changes were the genetic ancestors of Ukrainians and other European farm ers. They formed and strengthened the high moral archetype, which in the Eneolithic spread to most of Europe. The fact of genocide of these farmers by the ancestors of modern Europeans in the time interval 5.5-3.5 thousand years ago, which destroyed the humanistic paradigm in the West is given. It has survived only in the East in Trypillia and part of the Slavic world. The further history of the West is marked by outstanding anti-humanism to the present day, attempts to impose its worldview and values on Ukrainians and other custodians of the ancient archetype. Attempts do not stop even now, as the West imposes unacceptable principles of behavior on Ukraine, trying to slow down progress through economic and educational regulations and advice. The West has no right to teach, because it is not the West, but our ancestors carried out the first Indo-European spiritualization and started the New Noospiritualization-XXI.

Single-Cell Multi-Omics Reveals the Genetic, Cellular and Molecular Landscape of TP53 Mutated Leukemic Transformation in MPN

Single-Cell Multi-Omics Reveals the Genetic, Cellular and Molecular Landscape of TP53 Mutated Leukemic Transformation in MPN

European Carnival: traditions and nowadays

The problems of functioning of carnival traditions in the countries of Western Europe are examined in the given article. The ancient holidays of Dionysius and Saturnalia are the genetic ancestors, these were the periods when golden age seemed to be approaching the earth – the kingdom of universal equality and freedom. The carnival became a mass folk holiday with street processions, games, and theatrical performances in masks in the Middle Ages due to the development of European self-governing cities and the formation of the bourgeois class. Carnival theory is a field of active scientific discussion. While criticizing the vulnerable aspects of the carnival concept of M. Bakhtin, a representative of the international scientific community, they recognize the priority of the component structure of the public square laughter culture revealed by him. Inversion is the main idea of carnival illustrates change of the age, gender, social status of the participants of the festive event. One might receive a comprehensive knowledge of the international fund of carnival forms while analyzing its national variants. Taking this into account, the researcher might reveal the genesis and historical transformation of the most popular European carnivals, which are regularly performed in such cities as Venice, Cologne, Bensch, London. The European Carnival is the antithesis of a totalitarian holiday, which is characterized by excessive seriousness, false pathos, a stereotypical set of ideological slogans and clichйs. The experience of organizing carnival entertainment is interesting as an example of democratic festive communication, a bright artistic and aesthetic phenomenon, an example of successful self-organization of local communities.

Hierarchies of connection: on the inheritance argument for slavery reparations

ABSTRACT I reconsider and enhance a somewhat neglected argument within the domains of reparations for slavery and black reparations. That argument is for compensating present-day descendants of enslaved persons for wrongs done to their genetic ancestors, based on the inheritance of rights to compensation. After highlighting some of its virtues, some questions for it on which I remain agnostic, and some outright problems, I offer three desiderata for an elaboration of the argument: stronger African American claims, meaningful connection, and material-structural sensitivity. To satisfy these without ad-hocness, I motivate seven ‘hierarchies of connection’ between heir and predecessor via a series of thought-experiments involving ordinary inheritance of an estate. Moreover, I suggest that the elaborated version of the inheritance argument might be harder for good-faith political conservatives to dismiss than other pro-reparations arguments. Finally, I address an objection by modifying my view about the kind of right that will be held by descendants of enslaved persons if the argument succeeds.

KAJIAN APLIKASI TEKNIK INSEMINASI BUATAN DALAM PENINGKATAN GENETIK BOBOT BADAN TERNAK SAPI PERANAKAN ONGOLE DI SULAWESI UTARA

THE STUDY OF ARTIFICIAL INSEMINATION APPLICATION ON GENETIC IMPROVEMENT OF LIVE WEIGHT IN ONGOLE GRADE CATTLE AT NORTH SULAWESI PROVINCE. This research was conducted to evaluate the effective application of artificial insemination compared with natural breeding on genetic improvement by grading up system involving semen sourced from Ongole bull for the Indonesian-grade cattle at rural areas in Minahasa regency of North Sulawesi province, Indonesia. Data on animal live weight were collected from all cows (n= 404) kept by the traditional household farmers. Data of the cows were corrected by adjusting for the six years old of age. Breeding of beef genetic ancestors used the natural breeding (NB) and the artificial insemination (AI), divided into three cow groups with the first group of NB-mating without grading up (G0 cows), the second group of AI-mating with grading up using semen of Ongole bull for the first generation (G1 cows), and the third group of AI-mating with grading up using semen of Ongole bull for the second generation (G2 cows). The genetic improvements from breeding program of each G0, G1 and G2 were analyzed involving the selection intensity (i), the accuracy of selection (r), the genetic standard deviation of the trait under selection (SDg), and the generation interval (L) expressed in years. Results of this study showed that the critical components was the genetic development of local beef cattle by grading up using semen of the selected elite Ongole bull mated by AI method producing G2 in North Sulawesi province of Indonesia. This method increased genetically four hundred percents of live weight per year under 48% to 10% proportions of elite cows at the truncation points from the animal population compared with those of the natural mating of G0 in increasing genetic development for animal genetically live weight per year.Key Words: artificial insemination, genetic development, Indonesian local-grade cattle, Ongole breed bull

Abstract 3335: Innovative mathematical model links TRPV6 genotype to high triple negative breast cancer mortality rate in African-American females

Abstract INTRODUCTION: The mortality rate for African-American (AA) females is 4 times that of Whites due to the former’s higher susceptibility to Triple Negative Breast Cancer (TNBC). This study suggests that the African/ancestral TRPV6 calcium ion channel may be more calcium-absorbent than the European/derived TRPV6 variant. The 800 mg. daily calcium intake of AA women is twice that of their low-osteoporotic Niger-Kordofanian ancestors. This maladaptation may expose AA females’ mammary tissue to free calcium ions in excess of biological need. Ca2+ flooding appears to trigger over-expression of TRPV6 transcript, which becomes a biomarker for estrogen receptor (ER)-negative breast tumors. Therefore, this study introduces a Genetic-Population Specific Mathematical Model (GPs Mathematical Model), which identifies the ancestral TRPV6 calcium ion channel in AA females as a novel therapeutic target for TNBC and suggests TNBC-avoidant dietary guidelines for this ethnic population. . METHODS: The GPs Mathematical Model correlates ratios of DNA ancestry and calcium intake levels per genetic population. An interactive map based on data from 74 countries provided global calcium intake. Retrospective data sets on the genetic ancestry of 5,269 self-described African Americans, 8,663 Latinos, and 148,789 European Americans were correlated to the 1000 Genomes Project data. RESULTS: This Model identifies a normal range of dietary calcium consumption for AAs. The admixture ratio of this population is on average, 0.74 Niger-Kordofanian DNA; 0.24 Northern European DNA; 0.01 Native American DNA. Nutritional studies indicate that the average daily calcium intake for healthy Niger-Kordofanians, Northern Europeans and Native Americans are 200 to 400 mg, 1000 to 1200 mg, and 1100 mg. respectively or 0.75 (NK DNA Ancestry (200,400) + 0.24 NE DNA Ancestry (1000, 1200) + 0.01 NA DNA Ancestry(1100) = a range from 401 to 599, averaged to 500 mg/calcium/day. This Model shows that the calcium intake of AA females is 160% to 240% higher than the theoretical value derived from this ethnic group’s genetic ancestry. SUMMARY: This Genetic Population-Specific Mathematical Model suggests that the higher calcium intake of AA females relative to their genetic ancestors may create hyper-reactivity of ancestral TRPV6 leading to TNBC. CONCLUSION: Dietary calcium intake in excess of biological needs may trigger AA females’ high susceptibility to “TRPV6-expressing” Triple Negative Breast Cancer. The Genetic Population-Specific Mathematical Model provides an AA set-point of 500mg/d for dietary calcium intake, which is 0.375 lower than this ethnic population’s average consumption of 800 mg/calcium/day. The use of TRPV6 inhibitors should be tried in order to control the disease. In addition, a reduction in dietary calcium may have a prophylactic effect on this population's high susceptibility to TNBC. Note: This abstract was not presented at the meeting. Citation Format: Constance B. Hilliard. Innovative mathematical model links TRPV6 genotype to high triple negative breast cancer mortality rate in African-American females [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3335.

A law enforcement intelligence framework for use in predictive DNA phenotyping

ABSTRACTAnalysis of information about physical characteristics, biogeographical ancestry or common genetic ancestors from crime scene DNA is a technique aimed at informing an intelligence process, rather than obtaining evidence for a criminal trial. This intelligence supports tactical or operational decision-making. Like other forms of intelligence there is a risk for it to be misconstrued or for its investigative value to be misunderstood. The potential for intelligence derived from DNA to divert investigative resources or result in unnecessary intrusions into individual privacy can be mitigated by applying an appropriate intelligence doctrine. Establishing an appropriate framework could reduce the need for government regulation of these emerging capabilities in the context of law enforcement use.

Emergence/Subsidence Histories Along the Carnegie and Cocos Ridges and Their Bearing Upon Biological Speciation in the Galápagos

AbstractUsing plate motion reconstructions for the Nazca, Cocos, and South American plates in relation to the Galápagos hotspot, we find that age‐depth dependence of bathymetry, Galápagos plume dynamic topography, crustal relaxation, and magmatic production permit reasonable estimates for the subsidence of former islands along the Carnegie and Cocos Ridges. Our dynamic topography estimates are partially based upon geodynamic theory (fluid mechanics and elasticity) and also upon detailed bathymetric observations and analysis. For three different target areas over Carnegie Ridge and two over Cocos Ridge, we infer subaerial landmasses over the past ~20 Ma. We provide rough estimates of the surface areas of these paleo‐archipelagos, which were comparable to that of the present‐day Galápagos archipelago. We construct a history of emerged (paleo‐island) topography along the conjugate pair Carnegie‐Cocos hotspot tracks and infer that significant subaerial landscapes existed for at least the past ~20 Ma. The genetic ancestors of endemic faunal species in Galápagos (e.g., marine iguanas) migrated away from South America, genetically diverging from their land counterparts much earlier than the age of the present Galápagos Islands (~3 Ma). At 16.5 Ma, the total emerged landmass on the Carnegie Ridge alone may have been ~2.5 times that of the current Galápagos archipelago. (The conjugate landmass along the Cocos Ridge has been subducted.) We propose that this large landmass, at least one‐fourth the size of Iceland, be called Darwinia in recognition of its importance in the evolution of some Galápagos endemic flora and fauna made famous by Darwin's explorations.

The Anzick genome proves Clovis is first, after all

The close relatives who buried the Anzick infant ca. 12,800 cal BP made classic Clovis tools and were unequivocally the lineal genetic ancestors of all the living Native peoples of southern North America, Central America, and South America. Clovis-derived Fell I fishtail points track the rapid southward migration of this ancestral population all the way to Tierra del Fuego. Any hypothesized earlier populations, if they (improbably) ever existed, must have been replaced or genetically swamped by these Clovis descendants.

Spread of pedigree versus genetic ancestry in spatially distributed populations

Ancestral processes are fundamental to modern population genetics and spatial structure has been the subject of intense interest for many years. Despite this interest, almost nothing is known about the distribution of the locations of pedigree or genetic ancestors. Using both spatially continuous and stepping-stone models, we show that the distribution of pedigree ancestors approaches a travelling wave, for which we develop two alternative approximations. The speed and width of the wave are sensitive to the local details of the model. After a short time, genetic ancestors spread far more slowly than pedigree ancestors, ultimately diffusing out with radius ∼t rather than spreading at constant speed. In contrast to the wave of pedigree ancestors, the spread of genetic ancestry is insensitive to the local details of the models.

The existence and abundance of ghost ancestors in biparental populations

In a randomly-mating biparental population of size N there are, with high probability, individuals who are genealogical ancestors of every extant individual within approximately log2(N) generations into the past. We use this result of J. Chang to prove a curious corollary under standard models of recombination: there exist, with high probability, individuals within a constant multiple of log2(N) generations into the past who are simultaneously (i) genealogical ancestors of each of the individuals at the present, and (ii) genetic ancestors to none of the individuals at the present. Such ancestral individuals–ancestors of everyone today that left no genetic trace–represent ‘ghost’ ancestors in a strong sense. In this short note, we use simple analytical argument and simulations to estimate how many such individuals exist in finite Wright–Fisher populations.

Genomics Recapitulates History in Europe

Genomics Recapitulates History in Europe

The Geography of Recent Genetic Ancestry across Europe

Author SummaryFew of us know our family histories more than a few generations back. It is therefore easy to overlook the fact that we are all distant cousins, related to one another via a vast network of relationships. Here we use genome-wide data from European individuals to investigate these relationships over the past 3,000 years, by looking for long stretches of genome that are shared between pairs of individuals through their inheritance from common genetic ancestors. We quantify this ubiquitous recent common ancestry, showing for instance that even pairs of individuals from opposite ends of Europe share hundreds of genetic common ancestors over this time period. Despite this degree of commonality, there are also striking regional differences. Southeastern Europeans, for example, share large numbers of common ancestors that date roughly to the era of the Slavic and Hunnic expansions around 1,500 years ago, while most common ancestors that Italians share with other populations lived longer than 2,500 years ago. The study of long stretches of shared genetic material promises to uncover rich information about many aspects of recent population history.

Ionotropic and metabotropic mechanisms in chemoreception: 'chance or design'?

Chemosensory receptors convert an enormous diversity of chemical signals from the external world into a common language of electrical activity in the brain. Mammals and insects use several families of transmembrane receptor proteins to recognize distinct classes of volatile and non-volatile chemicals that are produced by conspecifics or other environmental sources. A comparison of the signalling mechanisms of mammalian and insect receptors has revealed an unexpected functional distinction: mammals rely almost exclusively on metabotropic ligand-binding receptors, which use second messenger signalling cascades to indirectly activate ion channels, whereas insects use ionotropic receptors, which are gated directly by chemical stimuli, thereby leading to neuronal depolarization. In this review, we consider possible reasons for this dichotomy, taking into account biophysical, cell biological, ecological and evolutionary influences on how information is extracted from chemosensory cues by these animal classes.

Overcoming Bias in the Deliberations of Distributed Teams

Human decision making is subject to a variety of cognitive and affective processes that can significantly impact the nature and quality of the resulting decisions. While commonly referred to as decision making ‘biases’, these processes evolved to satisfy important needs of our genetic ancestors. For example, heuristics that reduce the time and effort required to make decisions may be beneficial in a naturalistic environment that rewards speed and efficiency over precision or perfection. Unfortunately, the modern world has different performance criteria and our cognitive processes have not evolved fast enough to adapt. One example is the geographically distributed team, composed of individuals who communicate using technologies such as email, telephone, and videoconferencing to accomplish business-related objectives. While speed remains important in this environment, precision and accuracy are often the most relevant performance metrics. This paper presents a detailed description of several cognitive and affective processes that are particularly troublesome for geographically distributed teams when deliberating to reach a team consensus and outlines some technological and procedural interventions that can improve the quality of their decision making.

Assisted human reproduction offspring and the fundamental right to identity: the recognition of the right to know one's origins under the European Convention of Human Rights.

An individual's right to know about their own origins entails a legal system that provides judicial guarantees that make effective the right to know about their genetic ancestors. This is part of the fundamental right to identity and has its basis in the principles of autonomy and dignity: an individual's right to knowledge of their genetic origins is implicitly recognized by article 8 of the European Convention for the Protection of Human Rights and Fundamental Freedoms. As discussed in this paper, even though the European Court of Human Rights has not yet addressed this particular issue, the European legal systems that protect the anonymity of gamete donors and/or embryo donors appear to infringe an individual's right to genetic knowledge and, consequently, breaches Article 8 of the European Convention on Human Rights.