Admixture Models and the Breeding Systems of H. S. Jennings: A<i>GENETICS</i>Connection

Rosenberg, Noah A.

doi:10.1534/genetics.115.181057

Cited by 10 publications

(8 citation statements)

References 23 publications

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“…The optimum number of clusters ( K ) was processed and identified by STRUCTURE HARVESTER through comparing log probabilities of data for each value of K (Earl & Vonholdt, 2012; Stephens & Pritchard, 2003). The output of structure analyses was visualized using the software CLUMPP v1.1.2 (Kopelman, Mayzel, Jakobsson, Rosenberg, & Mayrose, 2015) and DISTRUCT v1.1 (Rosenberg, 2016). Data were input in an Excel spreadsheet in order to carry out statistical analysis and to make figures depicting genetic diversity and cultivar diversity of C. reticulata .…”

Section: Methodsmentioning

confidence: 99%

Genetic diversity, population structure, and traditional culture of Camellia reticulata

Tong

Huang

Riek³

et al. 2017

Ecology and Evolution

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Camellia reticulata is an arbor tree that has been cultivated in southwestern China by various sociolinguistic groups for esthetic purposes as well as to derive an edible seed oil. This study examined the influence of management, socio‐economic factors, and religion on the genetic diversity patterns of Camellia reticulata utilizing a combination of ethnobotanical and molecular genetic approaches. Semi‐structured interviews and key informant interviews were carried out with local communities in China's Yunnan Province. We collected plant material (n = 190 individuals) from five populations at study sites using single‐dose AFLP markers in order to access the genetic diversity within and between populations. A total of 387 DNA fragments were produced by four AFLP primer sets. All DNA fragments were found to be polymorphic (100%). A relatively high level of genetic diversity was revealed in C. reticulata samples at both the species (H sp = 0.3397, I sp = 0.5236) and population (percentage of polymorphic loci = 85.63%, H pop = 0.2937, I pop = 0.4421) levels. Findings further revealed a relatively high degree of genetic diversity within C. reticulata populations (Analysis of Molecular Variance = 96.31%). The higher genetic diversity within populations than among populations of C. reticulata from different geographies is likely due to the cultural and social influences associated with its long cultivation history for esthetic and culinary purposes by diverse sociolinguistic groups. This study highlights the influence of human management, socio‐economic factors, and other cultural variables on the genetic and morphological diversity of C. reticulata at a regional level. Findings emphasize the important role of traditional culture on the conservation and utilization of plant genetic diversity.

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Section: Methodsmentioning

confidence: 99%

Genetic diversity, population structure, and traditional culture of Camellia reticulata

Tong

Huang

Riek³

et al. 2017

Ecology and Evolution

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“…However, the nature of X chromosome inheritance means that it can clarify details of the relationships among individuals and be informative about sex-specific demography and admixture histories in ways that autosomes cannot (Ramachandran et al 2004(Ramachandran et al , 2008Pool and Nielsen 2007;Bustamante and Ramachandran 2009;Bryc et al 2010;Goldberg and Rosenberg 2015;Rosenberg 2016;Shringarpure et al 2016).…”

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confidence: 99%

A Genealogical Look at Shared Ancestry on the X Chromosome

2016

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Close relatives can share large segments of their genome identical by descent (IBD) that can be identified in genome-wide polymorphism data sets. There are a range of methods to use these IBD segments to identify relatives and estimate their relationship. These methods have focused on sharing on the autosomes, as they provide a rich source of information about genealogical relationships. We hope to learn additional information about recent ancestry through shared IBD segments on the X chromosome, but currently lack the theoretical framework to use this information fully. Here, we fill this gap by developing probability distributions for the number and length of X chromosome segments shared IBD between an individual and an ancestor k generations back, as well as between half-and full-cousin relationships. Due to the inheritance pattern of the X and the fact that X homologous recombination occurs only in females (outside of the pseudoautosomal regions), the number of females along a genealogical lineage is a key quantity for understanding the number and length of the IBD segments shared among relatives. When inferring relationships among individuals, the number of female ancestors along a genealogical lineage will often be unknown. Therefore, our IBD segment length and number distributions marginalize over this unknown number of recombinational meioses through a distribution of recombinational meioses we derive. By using Bayes' theorem to invert these distributions, we can estimate the number of female ancestors between two relatives, giving us details about the genealogical relations between individuals not possible with autosomal data alone.

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“…While autosomal allele frequencies reach HWE within a single generation, it is well known that for X, in case male and female allele frequencies initially differ, equilibrium (in an infinite population) is only asymptotically reached (Jennings 1916;Rosenberg 2016). The classical equations describing the evolution of allele frequencies on X, for an infinite population, are,…”

Section: Introductionmentioning

confidence: 99%

A test for deviations from expected genotype frequencies on the X chromosome for sex-biased admixed populations

Backenroth

Carmi

2019

Heredity

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Genome-wide scans for deviations from expected genotype frequencies, as determined by the Hardy-Weinberg equilibrium (HWE), are commonly applied to detect genotyping errors and deviations from random mating. In contrast to the autosomes, genotype frequencies on the X chromosome do not reach HWE within a single generation. Instead, if allele frequencies in males and females initially differ, they oscillate for a few generations toward equilibrium. Allele frequency differences between the sexes are expected in populations that have experienced recent sex-biased admixture, namely, their male and female founders differed in ancestry. Sex-biased admixture does not allow testing for HWE on X, because deviations are naturally expected, even under random mating (post admixture) and error-free genotyping. In this paper, we develop a likelihood ratio test and a χ 2 test to detect deviations from expected genotype frequencies on X, beyond natural deviations due to sex-biased admixture. We demonstrate by simulations that our tests are powerful for detecting deviations due to nonrandom mating, while at the same time they do not reject the null under historical sex-biased admixture and random mating thereafter. We also demonstrate that when applied to 1000 Genomes project populations, our likelihood ratio test rejects fewer SNPs than other tests, but we describe limitations in the interpretation of the results.

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Admixture Models and the Breeding Systems of H. S. Jennings: AGENETICSConnection

Cited by 10 publications

References 23 publications

Genetic diversity, population structure, and traditional culture of Camellia reticulata

Genetic diversity, population structure, and traditional culture of Camellia reticulata

A Genealogical Look at Shared Ancestry on the X Chromosome

A test for deviations from expected genotype frequencies on the X chromosome for sex-biased admixed populations

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