scholarly journals The kinship matrix: inferring the kinship structure of a population from its demography

2021 ◽  
Author(s):  
Christophe F. D. Coste ◽  
François Bienvenu ◽  
Victor Ronget ◽  
Juan‐Pablo Ramirez‐Loza ◽  
Sarah Cubaynes ◽  
...  
Keyword(s):  
Kinship Matrix ◽  
Kinship Structure

scholarly journals The Kinship Matrix: Inferring the Kinship Structure of a Population From Its Demography

2021 ◽  
Author(s):  
Christophe F. D. Coste ◽  
François Bienvenu ◽  
Victor Ronget ◽  
Sarah Cubaynes ◽  
Samuel Pavard
Keyword(s):  
Population Dynamics ◽  
Life Cycle ◽  
General Formula ◽  
Population Model ◽  
Matrix Population Model ◽  
Expected Number ◽  
Kinship Matrix ◽  
Structured Population ◽  
Kinship Structure ◽  
General Method

AbstractThe familial structure of a population and the relatedness of its individuals are determined by its demography. There is, however, no general method to infer kinship directly from the life-cycle of a structured population. Yet this question is central to fields such as ecology, evolution and conservation, especially in contexts where there is a strong interdependence between familial structure and population dynamics. Here, we give a general formula to compute, from any matrix population model, the expected number of arbitrary kin (sisters, nieces, cousins, etc) of a focal individual ego, structured by the class of ego and of its kin. Central to our approach are classic but little-used tools known as genealogical matrices, which we combine in a new way. Our method can be used to obtain both individual-based and population-wide metrics of kinship, as we illustrate. It also makes it possible to analyze the sensitivity of the kinship structure to the traits implemented in the model.

THE PARTICULAR STRUCTURAL TRAITS OF THE MIGRATION CATHOLIC COMMUNITY IN THE SOUTHERN VIETNAM

2010 ◽  
Vol 13 (3) ◽  
pp. 5-20
Author(s):  
Loc Duc Nguyen
Keyword(s):  
Historical Context ◽  
Residential Area ◽  
Religious Community ◽  
Viet Nam ◽  
Religious Organization ◽  
Religious Activities ◽  
Economic Activities ◽  
Southern Vietnam ◽  
Kinship Structure ◽  
Structural Traits

The Vietnamese Catholic community is not only a religious community but also a traditional village with relationships based on kinship and/or sharing the same residential area, similar economic activities, and religious activities. In this essay, we are interested in examining migrating Catholic communities which were shaped and reshaped within the historical context of Viet Nam war in 1954. They were established after the migration of millions of Catholics from Northern to Southern Viet Nam immediately after Geneva Agreement in 1954. Therefore, by examining the particular structural traits of the emigration Catholic Communities we attempt to reconstruct the reproducing process of village structure based on the communities’ triple structure: kinship structure, governmental structure and religious organization.

scholarly journals Effects of kinship correction on inflation of genetic interaction statistics in commonly used mouse populations

2021 ◽  
Author(s):  
Anna L Tyler ◽  
Baha El Kassaby ◽  
Georgi Kolishovski ◽  
Jake Emerson ◽  
Ann E Wells ◽  
...  
Keyword(s):  
Mixed Model ◽  
Linear Mixed Model ◽  
Genetic Interaction ◽  
Recombinant Inbred Lines ◽  
Test Statistics ◽  
Test Statistic ◽  
Kinship Matrix ◽  
Main Effect ◽  
Main Effects ◽  
Interaction Test

Abstract It is well understood that variation in relatedness among individuals, or kinship, can lead to false genetic associations. Multiple methods have been developed to adjust for kinship while maintaining power to detect true associations. However, relatively unstudied, are the effects of kinship on genetic interaction test statistics. Here we performed a survey of kinship effects on studies of six commonly used mouse populations. We measured inflation of main effect test statistics, genetic interaction test statistics, and interaction test statistics reparametrized by the Combined Analysis of Pleiotropy and Epistasis (CAPE). We also performed linear mixed model (LMM) kinship corrections using two types of kinship matrix: an overall kinship matrix calculated from the full set of genotyped markers, and a reduced kinship matrix, which left out markers on the chromosome(s) being tested. We found that test statistic inflation varied across populations and was driven largely by linkage disequilibrium. In contrast, there was no observable inflation in the genetic interaction test statistics. CAPE statistics were inflated at a level in between that of the main effects and the interaction effects. The overall kinship matrix overcorrected the inflation of main effect statistics relative to the reduced kinship matrix. The two types of kinship matrices had similar effects on the interaction statistics and CAPE statistics, although the overall kinship matrix trended toward a more severe correction. In conclusion, we recommend using a LMM kinship correction for both main effects and genetic interactions and further recommend that the kinship matrix be calculated from a reduced set of markers in which the chromosomes being tested are omitted from the calculation. This is particularly important in populations with substantial population structure, such as recombinant inbred lines in which genomic replicates are used.

Why Was There a Transition from an Elementary Kinship Structure to a Complex One?

2017 ◽  
Author(s):  
Paul Valentine ◽  
Lionel D. Sims
Keyword(s):  
Social Transformation ◽  
Cousin Marriage ◽  
Historical Material ◽  
Government Project ◽  
Kinship Structure ◽  
The Government ◽  
Parallel Case ◽  
Rubber Boom ◽  
San Carlos ◽  
The Village

During the 1930s in the Venezuelan village of San Carlos de Río Negro, the Baré practiced cross-cousin marriage. However, by the 1980s they married hypergamously among the Curripaco, Geral, and Criollos, all of whom had recently migrated to the village. There is considerable historical material on San Carlos, which when coupled with fieldwork, facilitate the formulation of a number of hypotheses to test what best accounts for this transformation of marital rules. Lévi-Strauss predicted the causes of the breakdown of elementary kinship structures and the creation of complex ones; this chapter suggests an alternative scenario. In a parallel case, Curripaco women migrated to San Carlos in the 1970s and 1980s, could marry someone employed directly or indirectly in the government project, Codesur (Comisión para el Desarrollo del Sur), and became incorporated into the complex kinship structure of this ex–rubber boom village. This chapter suggests their social transformation sheds light on the Baré transformation of some forty years earlier.

scholarly journals GPU empowered pipelines for calculating genome-wide kinship matrices with ultra-high dimensional genetic variants and facilitating 1D and 2D GWAS

2019 ◽  
Vol 2 (1) ◽  
Author(s):  
Wenchao Zhang ◽  
Xinbin Dai ◽  
Shizhong Xu ◽  
Patrick X Zhao
Keyword(s):  
Genetic Variants ◽  
High Performance ◽  
Genome Wide Association Study ◽  
Graphics Processing Unit ◽  
High Dimensional ◽  
Processing Unit ◽  
Kinship Matrix ◽  
Matrix Operations ◽  
Genome Wide ◽  
Matrix Calculation

Abstract Genome-wide association study (GWAS) is a powerful approach that has revolutionized the field of quantitative genetics. Two-dimensional GWAS that accounts for epistatic genetic effects needs to consider the effects of marker pairs, thus quadratic genetic variants, compared to one-dimensional GWAS that accounts for individual genetic variants. Calculating genome-wide kinship matrices in GWAS that account for relationships among individuals represented by ultra-high dimensional genetic variants is computationally challenging. Fortunately, kinship matrix calculation involves pure matrix operations and the algorithms can be parallelized, particular on graphics processing unit (GPU)-empowered high-performance computing (HPC) architectures. We have devised a new method and two pipelines: KMC1D and KMC2D for kinship matrix calculation with high-dimensional genetic variants, respectively, facilitating 1D and 2D GWAS analyses. We first divide the ultra-high-dimensional markers and marker pairs into successive blocks. We then calculate the kinship matrix for each block and merge together the block-wise kinship matrices to form the genome-wide kinship matrix. All the matrix operations have been parallelized using GPU kernels on our NVIDIA GPU-accelerated server platform. The performance analyses show that the calculation speed of KMC1D and KMC2D can be accelerated by 100–400 times over the conventional CPU-based computing.

scholarly journals Monotocy and the evolution of plural breeding in mammals

2020 ◽  
Vol 31 (4) ◽  
pp. 943-949 ◽  
Author(s):  
Dieter Lukas ◽  
Tim Clutton-Brock
Keyword(s):  
Life History ◽  
Evolutionary Transitions ◽  
Life History Parameters ◽  
Interspecific Differences ◽  
Risk Of Predation ◽  
Size Stability ◽  
Distribution Of Resources ◽  
Kinship Structure ◽  
Competition For Food ◽  
Plural Breeding

Abstract In many mammals, breeding females are intolerant of each other and seldom associate closely but, in some, they aggregate in groups that vary in size, stability, and kinship structure. Aggregation frequently increases competition for food, and interspecific differences in female sociality among mammals are commonly attributed to contrasts in ecological parameters, including variation in activity timing, the distribution of resources, as well as the risk of predation. However, there is increasing indication that differences in female sociality are also associated with phylogenetic relationships and with contrasts in life-history parameters. We show here that evolutionary transitions from systems where breeding females usually occupy separate ranges (“singular breeding”) to systems where breeding females usually aggregate (“plural breeding”) have occurred more frequently in monotocous lineages where females produce single young than in polytocous ones where they produce litters. A likely explanation of this association is that competition between breeding females for resources is reduced where they produce single young and is more intense where they produce litters. Our findings reinforce evidence that variation in life-history parameters plays an important role in shaping the evolution of social behavior.

scholarly journals Contrasts in kinship structure in mammalian societies

2020 ◽  
Vol 31 (4) ◽  
pp. 971-977 ◽  
Author(s):  
Mark Dyble ◽  
Tim H Clutton-Brock
Keyword(s):  
Social Groups ◽  
Theoretical Models ◽  
Competitive Behavior ◽  
Factors Affecting ◽  
Interspecific Differences ◽  
Wide Range ◽  
Group Members ◽  
Relative Rarity ◽  
Kinship Structure ◽  
Insight Into

Abstract Comparative studies of mammals confirm Hamilton’s prediction that differences in cooperative and competitive behavior across species will be related to contrasts in kinship between group members. Although theoretical models have explored the factors affecting kinship within social groups, few have analyzed the causes of contrasts in kinship among related species. Here, we describe interspecific differences in average kinship between group members among social mammals and show that a simple mathematical model that includes the number of breeding females, male reproductive skew, and litter size successfully predicts ~95% of observed variation in average kinship between group members across a sample of mammals. Our model shows that a wide range of conditions can generate groups with low average relatedness but only a small and rather specific set of conditions are likely to generate high average levels of relatedness between their members, providing insight into the relative rarity of advanced forms of cooperation in mammalian societies.

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