Genealogical Networks Research Articles

The persistent homology of genealogical networks

Genealogical networks (i.e. family trees) are of growing interest, with the largest known data sets now including well over one billion individuals. Interest in family history also supports an 8.5 billion dollar industry whose size is projected to double within 7 years [FutureWise report HC-1137]. Yet little mathematical attention has been paid to the complex network properties of genealogical networks, especially at large scales. The structure of genealogical networks is of particular interest due to the practice of forming unions, e.g. marriages, that are typically well outside one’s immediate family. In most other networks, including other social networks, no equivalent restriction exists on the distance at which relationships form. To study the effect this has on genealogical networks we use persistent homology to identify and compare the structure of 101 genealogical and 31 other social networks. Specifically, we introduce the notion of a network’s persistence curve, which encodes the network’s set of persistence intervals. We find that the persistence curves of genealogical networks have a distinct structure when compared to other social networks. This difference in structure also extends to subnetworks of genealogical and social networks suggesting that, even with incomplete data, persistent homology can be used to meaningfully analyze genealogical networks. Here we also describe how concepts from genealogical networks, such as common ancestor cycles, are represented using persistent homology. We expect that persistent homology tools will become increasingly important in genealogical exploration as popular interest in ancestry research continues to expand.

Probing the Gendered History of Aegean Survey Archaeology

Probing the Gendered History of Aegean Survey Archaeology

On Dankwa's Gift

On Dankwa's Gift

Power law dynamics in genealogical graphs

Several populational networks present complex topologies when implemented in evolutionary algorithms. A common feature of these topologies is the emergence of a power law. Power law behavior with different scaling factors can also be observed in genealogical networks, but we still cannot satisfactorily describe its dynamics or its relation to population evolution over time. In this paper, we use an algorithm to measure the impact of individuals in several numerical populations and study its dynamics of evolution through nonextensive statistics. Like this, we show evidence that the observed emergence of power law has a dynamic behavior over time. This dynamic development can be described using a family of q-exponential distributions whose parameters are time-dependent and follow a specific pattern. We also show evidence that elitism significantly influences the power law scaling factors observed. These results imply that the different power law shapes and deviations observed in genealogical networks are static images of a time-dependent dynamic development that can be satisfactorily described using q-exponential distributions.

Private Genetic Genealogy Search

Genetic genealogy search has emerged as a powerful technique for identifying individuals by leveraging their genetic information and a genealogical network. The current practice relies on searching within a pre-constructed database containing genetic data from many individuals, and as such exposes those in the database to substantial privacy risks. Motivated by these privacy concerns, we propose a framework of genealogy search that takes into account the amount of privacy exposure. In contrast to the existing static approach of collecting a large amount of genetic data beforehand, we advocate for a new search paradigm whereby genetic samples are accessed in a sequential manner. Our results show that carefully designed sequential search procedures can significantly outperform existing static approaches in terms of the trade-off between cost and privacy exposure. We further characterize the optimal trade-off, and propose a family of search strategies that provably achieve the it over path- and grid-like networks. Finally, we validate our findings via numerical experiments on both real and synthetic genealogical networks and discuss the policy implications of our results.

A Genome Epidemiological Study of SARS-CoV-2 Introduction into Japan.

After the first case of coronavirus disease 2019 (COVID-19) in Japan on 15 January 2020, multiple nationwide COVID-19 clusters were identified by the end of February. The Japanese government focused on mitigating the emerging COVID-19 clusters by conducting active nationwide epidemiological surveillance. However, an increasing number of cases continued to appear until early April 2020, many with unclear infection routes and no recent history of travel outside Japan. We aimed to evaluate the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome sequences from the COVID-19 cases that appeared until early April 2020 and to characterize their genealogical networks in order to demonstrate possible routes of spread in Japan. Nasopharyngeal specimens were collected from patients, and reverse transcription-quantitative PCR tests for SARS-CoV-2 were performed. Positive RNA samples were subjected to whole-genome sequencing, and a haplotype network analysis was performed. Some of the primary clusters identified during January and February 2020 in Japan descended directly from the Wuhan-Hu-1-related isolates from China and other distinct clusters. Clusters were almost contained until mid-March; the haplotype network analysis demonstrated that the COVID-19 cases from late March through early April may have created an additional large cluster related to the outbreak in Europe, leading to additional spread within Japan. In conclusion, genome surveillance has suggested that there were at least two distinct SARS-CoV-2 introductions into Japan from China and other countries.IMPORTANCE This study aimed to evaluate the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome sequences from COVID-19 cases and to characterize their genealogical networks to demonstrate possible routes of spread in Japan. We found that there were at least two distinct SARS-CoV-2 introductions into Japan, initially from China and subsequently from other countries, including Europe. Our findings can help understand how SARS-CoV-2 entered Japan and contribute to increased knowledge of SARS-CoV-2 in Asia and its association with implemented stay-at-home/shelter-in-place/self-restraint/lockdown measures. This study suggested that it is necessary to formulate a more efficient containment strategy using real-time genome surveillance to support epidemiological field investigations in order to highlight potential infection linkages and mitigate the next wave of COVID-19 in Japan.

Types and Characteristics of Kyai Leadership Within Pesantren

This article attempts to explore types and characteristics of Kyai leadership within Pesantren. This library research found that there are 412 articles related to the leadership of Kyai. Based on the inclusion criteria, there are 12 articles yielded as the material sources. The appropriate data found in the searching machine is analyzed accordingly to the research questions by employing a qualitative approach. Specifically, the types of Kyai leadership within Pesantren are charismatic, transformative, and democratic leaderships. The characteristics of Kyai leadership in Pesantren including having a strong and authoritative leadership character in maintaining Pesantren’s education and development; keeping the traditions, local principles and interacting with global values; having internal and external networks e.g a genealogical, ideological, historical, intellectual, theological, and spiritual networks in serving Islam and Indonesia. This research recommends for further researchers to address this study focuses on a networking of Kyai. The themes of Kyai’s intellectual networks, ideological networks, spiritual networks, theological network are highly recommended.

How Can We Know Wai-Horotiu—A Buried River? Cross-cultural Ethics and Civic Art

The complex interactions and ruptures between contemporary settler colonialism, environmental ethics, and Indigenous rights and worldviews often emerge in projects of civil engineering. The continued capture, control and burial of natural water courses in Aotearoa-New Zealand is a case in point, and exemplifies a failure to stay abreast of evolving understandings and renewed relationships we seek with our waterways, our ancestors. Wai-Horotiu stream used to run down what is now Queen Street, the main road in Auckland, Aotearoa-New Zealand’s largest city. Treasured by Māori as a source of wai (water) and mahinga kai (food), it is also the home of Horotiu, a taniwha or ancestral guardian—a literal ‘freshwater body’. However, as Tāmaki-Makaurau transitioned into Auckland city, Wai-Horotiu became denigrated; used as an open sewer by early settlers before being buried alive in the colonial process. How, now, can we know this buried waterway? Te Awa Tupua Act 2017 that affords the Whanganui River juristic personality and moral considerability offers one possible solution. It acknowledges that waterways, incorporating all their physical and metaphysical elements, exist in existential interlinks with Māori as part of their whakapapa (genealogical networks). This paper asks, can a corresponding and appropriate ethics of association and care be fostered in and expressed by the political descendants of British settlers (Pākehā) and later immigrants who live here under the auspices established by Te Tiriti o Waitangi in 1840? Here is a conversation between a Māori earth systems scientist and a Pākehā interdisciplinary scholar. Where Hikuroa speaks from and to direct whakapapa connections, beginning with pepeha, Lythberg’s narrative springboards from public art projects that facilitate more ways of knowing Wai-Horotiu. Together, we contend that a regard for Indigenous relationships with water can guide best practice for us all, and propose that creative practices can play a role in attaching people to place, and to waterways.

Quantum Artificial Life in an IBM Quantum Computer

We present the first experimental realization of a quantum artificial life algorithm in a quantum computer. The quantum biomimetic protocol encodes tailored quantum behaviors belonging to living systems, namely, self-replication, mutation, interaction between individuals, and death, into the cloud quantum computer IBM ibmqx4. In this experiment, entanglement spreads throughout generations of individuals, where genuine quantum information features are inherited through genealogical networks. As a pioneering proof-of-principle, experimental data fits the ideal model with accuracy. Thereafter, these and other models of quantum artificial life, for which no classical device may predict its quantum supremacy evolution, can be further explored in novel generations of quantum computers. Quantum biomimetics, quantum machine learning, and quantum artificial intelligence will move forward hand in hand through more elaborate levels of quantum complexity.

Modelling students’ knowledge organisation: Genealogical conceptual networks

Learning scientific knowledge is largely based on understanding what are its key concepts and how they are related. The relational structure of concepts also affects how concepts are introduced in teaching scientific knowledge. We model here how students organise their knowledge when they represent their understanding of how physics concepts are related. The model is based on assumptions that students use simple basic linking-motifs in introducing new concepts and mostly relate them to concepts that were introduced a few steps earlier, i.e. following a genealogical ordering. The resulting genealogical networks have relatively high local clustering coefficients of nodes but otherwise resemble networks obtained with an identical degree distribution of nodes but with random linking between them (i.e. the configuration-model). However, a few key nodes having a special structural role emerge and these nodes have a higher than average communicability betweenness centralities. These features agree with the empirically found properties of students’ concept networks.

Assessing global range expansion in a cryptic species complex: insights from the red seaweed genus Asparagopsis (Florideophyceae).

The mitochondrial genetic diversity, distribution and invasive potential of multiple cryptic operational taxonomic units (OTUs) of the red invasive seaweed Asparagopsis were assessed by studying introduced Mediterranean and Hawaiian populations. Invasive behavior of each Asparagopsis OTU was inferred from phylogeographic reconstructions, past historical demographic dynamics, recent range expansion assessments and future distributional predictions obtained from demographic models. Genealogical networks resolved Asparagopsis gametophytes and tetrasporophytes into four A.taxiformis and one A.armata cryptic OTUs. Falkenbergia isolates of A.taxiformis L3 were recovered for the first time in the western Mediterranean Sea and represent a new introduction for this area. Neutrality statistics supported past range expansion for A.taxiformis L1 and L2 in Hawaii. On the other hand, extreme geographic expansion and an increase in effective population size were found only for A.taxiformis L2 in the western Mediterranean Sea. Distribution models predicted shifts of the climatically suitable areas and population expansion for A.armata L1 and A.taxiformis L1 and L2. Our integrated study confirms a high invasive risk for A.taxiformis L1 and L2 in temperate and tropical areas. Despite the differences in predictions among modelling approaches, a number of regions were identified as zones with high invasion risk for A.taxiformis L2. Since range shifts are likely climate-driven phenomena, future invasive behavior cannot be excluded for the rest of the lineages.

Lagrangian relaxations for multiple network alignment

We propose a principled approach for the problem of aligning multiple partially overlapping networks. The objective is to map multiple graphs into a single graph while preserving vertex and edge similarities. The problem is inspired by the task of integrating partial views of a family tree (genealogical network) into one unified network, but it also has applications, for example, in social and biological networks. Our approach, called Flan, introduces the idea of generalizing the facility location problem by adding a non-linear term to capture edge similarities and to infer the underlying entity network. The problem is solved using an alternating optimization procedure with a Lagrangian relaxation. Flan has the advantage of being able to leverage prior information on the number of entities, so that when this information is available, Flan is shown to work robustly without the need to use any ground truth data for fine-tuning method parameters. Additionally, we present three multiple-network extensions to an existing state-of-the-art pairwise alignment method called Natalie. Extensive experiments on synthetic, as well as real-world datasets on social networks and genealogical networks, attest to the effectiveness of the proposed approaches which clearly outperform a popular multiple network alignment method called IsoRankN.

Painters and Paintings in the Early American South by Carolyn J. Weekley (review)

Reviewed by: Painters and Paintings in the Early American South by Carolyn J. Weekley Eleanor Jones Harvey (bio) Painters and Paintings in the Early American South Carolyn J. Weekley New Haven: Colonial Williamsburg Foundation in Association with Yale University Press, 2013 438 pp. Painters and Paintings in the Early American South is the culmination of forty years’ work, painstakingly assembled and presented by Carolyn J. Weekley. Her acknowledgments alone make clear the magnitude of this endeavor, providing a road map of the archives, museums, colleagues, and collectors with whom she has worked in pursuit of information crucial to an understanding of the fine arts in the southern colonies between 1564 and the 1790s. The result is a massive and thorough enumeration of the contributions painters made to early southern culture, a significant and lasting research resource relying heavily on primary archival material to ground our understanding of the network of patrons and artists active during this period. Weekley begins with the laudable premise that there is no “southern” style endemic to the works produced by early generations of American artists, and rightly concludes that the tendency toward ascribing specifically and uniquely southern characteristics to American art is in large part a legacy of the Civil War. I would further note that even more recently—during the Bicentennial of 1976—the promotion of civic and by extension regional pride prevailed over commemorating a more balanced view of our history. That bias is only now being seen for what it is—making clear the need for a corrective approach to understanding the complexity of American art from its inception to the present day. This is not to underestimate [End Page 576] the power of local preference and custom, or insist on a generic American style—but to point out that many of the artists discussed in this volume plied their trade up and down the thirteen colonies, and as Weekley notes, did not appreciably change their styles in so doing. But the Civil War did leave one daunting legacy with which Weekley grapples throughout her work: the often frustrating lack of records before the war, exacerbated by the lamentable destruction of records during and after it. The ragged economy in the post–Civil War years plays a supporting role here, as careful research on artwork and records across the South lagged well behind the scholarship devoted to art made in the northern colonies. As a result, Weekely’s career has been spent sleuthing everything she could find, each piece of information contributing to a better understanding of the cultural and aesthetic drivers during this period. Much of the information she has found takes the form of genealogical networks of southern families and the artists they patronized. There is, as a result, a steady flow of detailed and interconnected family histories, and at times the volume reads like a conversation about various extended family trees rather than an analysis of the artworks produced. There is a pragmatic reason for this close attention to family ties: whereas research on the key paintings and sitters in the northern colonies is vast, this volume represents the most comprehensive effort to date to account for a southern history of artistic practice. To readers steeped in and fascinated by genealogy, this book provides an impressive web of connections; for a lay reader seeking to understand the various roles the fine arts played in colonial life and in the transition to nationhood, it can be tough going. The text favors this genealogical approach; the extended captions on the paintings themselves provide only a modicum of art historical analysis of the artworks. Not surprisingly, then, the vast majority of paintings included as illustrations and described are portraits. Weekley has made every effort to include landscapes and coastal views wherever possible, but very few examples either survive or can be ascribed to an artist working in the South. A set of charming coastal marine views she includes as illustrations are made by an observing British artist—a reminder that landscape painting did not begin to flourish as a separate and significant genre until after the Revolution. (A parallel may be drawn between this and seventeenth-century Dutch landscape painting, which flourished...

Virtual Fieldwork: Modeling Observer Bias in Kinship and Marriage Alliance Networks

The morphological properties of genealogical and marriage alliance networks constitute a key to the understanding of matrimonial behavior and social norms, in particular where these norms have not been explicitly formalized. Their analysis, however, faces a major difficulty: the actual datasets which allow researchers to reconstruct kinship and alliance networks are generally subject to a marked observer bias, if only due to limitations of observer mobility and/or informant memory. This paper presents an agent based simulation method destined to evaluate the impact of this bias on some key indicators of kinship and alliance networks (such as matrimonial circuit frequencies). The method consists in explicitly simulating the exploration of a given network by a virtual observer, the bias being introduced by the observer's inclination for choosing informants who are more or less closely related to each other. The article presents the model for genealogical and for alliance networks, applies it to a series of artificial networks exhibiting some characteristic morphological patterns, and discusses the divergence of observed from real patterns for different kinds and degrees of observer bias. The methods presented have been implemented in the free software Puck 2.0.

Genealogical Avenues, Long-Distance Flows and Social Hierarchy: Hadramī Migrants in the Indonesian Diaspora

The article reflects on the role of genealogy in the process of Hadramī migration to Indonesia and explores the relation between genealogy and the construction of hierarchy and identity among diaspora Hadramīs. In addition to persons and ideas travelling along genealogical networks from the Hadramawt to Indonesia, the authors examine long-distance flows originating from Middle Eastern centres of Islamic learning, which were used to question a genealogically based social hierarchy. After discussing the flows and movements of the colonial period, our focus advances to the present, as we investigate the consequences of both new and renewed long-distance connections between Indonesia and the Hadramawt.

Internodons as equivalence classes in genealogical networks: building-blocks for a rigorous species concept

Among the options suggested in phylogenetic systematics to solve the species problem is the Hennigian or internodal species concept. This concept interprets species as parts of the genealogical network of individual organisms between two successive permanent splits or between a permanent split and an extinction event. Though this option is at present not favoured by phylogeneticists, we believe that, to solve the species problem, there is no alternative to finding a satisfactory partition of the genealogical network. In previous work a formal definition has been developed of Hennigian or internodal species (called internodons here), based on a logical relation between individual organisms. In this paper, we prove that this definition indeed partitions genealogical networks exhaustively into mutually exclusive entities, by showing that the defining relation is an equivalence relation. Although internodons should not themselves be seen as species, they are essential building-blocks for any satisfying species concept.

Permanent Splits as Speciation Events: A Formal Reconstruction of the Internodal Species Concept

The internodal species concept, which interprets a species as a part of the genealogical network between two permanent splits, is a good prima facie candidate to satisfy the intuition that species should at least be mutually exclusive. This paper develops a formal definition of internodal species: such a species is defined as a set of organisms of which each pair satisfies a conspecificity relation INT. Species so defined are mutually exclusive since INT is an equivalence relation. The relation INT is constructed out of only two primitive relations, parenthood and priority of birth. An algorithm is offered to determine, from their positions in the genealogical network, whether two given organisms belong to the same internodal species. This algorithm deals with asexual as well as sexual organisms and is so sharp as to place a species boundary between close relatives. It also enables us to define monophyletic groups and genealogical networks as sets of organisms. From its reconstruction we may conclude that the internodal species concept forms a firm basis for further development of a satisfactory species concept.