scholarly journals On the heterozygosity of an admixed population

2019 ◽  
Author(s):  
Simina M. Boca ◽  
Lucy Huang ◽  
Noah A. Rosenberg
Keyword(s):  
Genetic Variation ◽  
Genetic Variability ◽  
Genetic Variants ◽  
Simulated Data ◽  
Source Population ◽  
Admixed Population ◽  
Source Populations ◽  
Special Case

A population is termed admixed if its members possess recent ancestry from two or more separate sources. As a result of the fusion of source populations with different genetic variants, admixed populations can exhibit high levels of genetic variation, reflecting contributions of their multiple ancestral groups. For a model of an admixed population derived from K source groups, we obtain a relationship between its level of genetic variation, as measured by heterozygosity, and its proportions of admixture from the various source populations. We show that the heterozygosity of the admixed population is at least as great as that of the least heterozygous source population, and that it potentially exceeds the heterozygosities of all of the source populations. The admixture proportions that maximize the heterozygosity possible for an admixed population formed from a specified set of source populations are also obtained under specific conditions. We examine the special case of K = 2 source populations in detail, characterizing the maximal admixture in terms of the heterozygosities of the two source populations and the value of FST between them. In this case, the heterozygosity of the admixed population exceeds the maximal heterozygosity of the source groups if the divergence between them, measured by FST, is large enough, namely above a certain bound that is a function of the heterozygosities of the source groups. We present applications to simulated data as well as to data from human admixture scenarios, providing results useful for interpreting the properties of genetic variability in admixed populations.

scholarly journals Limited effects of source population identity and number on seagrass transplant performance

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e2972 ◽  
Author(s):  
Alyssa B. Novak ◽  
Holly K. Plaisted ◽  
Cynthia G. Hays ◽  
Randall A. Hughes
Keyword(s):  
Genetic Variation ◽  
Zostera Marina ◽  
Population Level ◽  
Shoot Density ◽  
Population Diversity ◽  
Multiple Source ◽  
Source Population ◽  
Post Transplantation ◽  
Home Site ◽  
Source Populations

Global declines in coastal foundation species highlight the importance of effective restoration. In this study, we examined the effects of source population identity and diversity (one vs. three sources per plot) on seagrass (Zostera marina) transplant success. The field experiment was replicated at two locations in Massachusetts with adjacent naturalZostera marinabeds to test for local adaptation and source diversity effects on shoot density. We also collected morphological and genetic data to characterize variation within and among source populations, and evaluate whether they were related to performance. Transplants grew and expanded until six months post-transplantation, but then steadily declined at both sites. Prior to declines, we observed variation in performance among source populations at one site that was related to morphological traits: the populations with the longest leaves had the highest shoot densities, whereas the population with the shortest leaves performed the worst at six months post-transplantation. In addition, multiple source plots at this same transplant site consistently had similar or higher shoot densities than single source plots, and shoots from weak-performing populations showed improved performance in multiple source plots. We found no evidence for home site advantage or benefits of population-level genetic variation in early transplant performance at either site. Our results show limited effects of source population on early transplant performance and suggest that factors (e.g., morphology) other than home site advantage and population genetic variation serve a role. Based on our overall findings that transplant success varied among source populations and that population diversity at the plot level had positive but limited effects on individual and plot performance, we support planting shoots from multiple source sites in combination to enhance transplant success, particularly in the absence of detailed information on individual source characteristics.

scholarly journals Assortative mating and the dynamical decoupling of genetic admixture levels from phenotypes that differ between source populations

2019 ◽  
Author(s):  
Jaehee Kim ◽  
Michael D. Edge ◽  
Amy Goldberg ◽  
Noah A. Rosenberg
Keyword(s):  
Assortative Mating ◽  
Genetic Architecture ◽  
Genetic Ancestry ◽  
Genetic Admixture ◽  
Human Populations ◽  
Source Population ◽  
Specific Source ◽  
Admixed Population ◽  
Source Populations ◽  
Over Time

AbstractSource populations for an admixed population can possess distinct patterns of genotype and pheno-type at the beginning of the admixture process. Such differences are sometimes taken to serve as markers of ancestry—that is, phenotypes that are initially associated with the ancestral background in one source population are taken to reflect ancestry in that population. Examples exist, however, in which genotypes or phenotypes initially associated with ancestry in one source population have decoupled from overall admixture levels, so that they no longer serve as proxies for genetic ancestry. We develop a mechanistic model for describing the joint dynamics of admixture levels and phenotype distributions in an admixed population. The approach includes a quantitative-genetic model that relates a phenotype to underlying loci that affect its trait value. We consider three forms of mating. First, individuals might assort in a manner that is independent of the overall genetic admixture level. Second, individuals might assort by a quantitative phenotype that is initially correlated with the genetic admixture level. Third, individuals might assort by the genetic admixture level itself. Under the model, we explore the relationship between genetic admixture level and phenotype over time, studying the effect on this relationship of the genetic architecture of the phenotype. We find that the decoupling of genetic ancestry and phenotype can occur surprisingly quickly, especially if the phenotype is driven by a small number of loci. We also find that positive assortative mating attenuates the process of dissociation in relation to a scenario in which mating is random with respect to genetic admixture and with respect to phenotype. The mechanistic framework suggests that in an admixed population, a trait that initially differed between source populations might be a reliable proxy for ancestry for only a short time, especially if the trait is determined by relatively few loci. The results are potentially relevant in admixed human populations, in which phenotypes that have a perceived correlation with ancestry might have social significance as ancestry markers, despite declining correlations with ancestry over time.Author SummaryAdmixed populations are populations that descend from two or more populations that had been separated for a long time at the beginning of the admixture process. The source populations typically possess distinct patterns of genotype and phenotype. Hence, early in the admixture process, phenotypes of admixed individuals can provide information about the extent to which these individuals possess ancestry in a specific source population. To study correlations between admixture levels and phenotypes that differ between source populations, we construct a genetic and phenotypic model of the dynamical process of admixture. Under the model, we show that correlations between admixture levels and these phenotypes dissipate over time—especially if the genetic architecture of the phenotypes involves only a small number of loci, or if mating in the admixed population is random with respect to both the admixture levels and the phenotypes. The result has the implication that a trait that once reflected ancestry in a specific source population might lose this ancestry correlation. As a consequence, in human populations, after a sufficient length of time, salient phenotypes that can have social meaning as ancestry markers might no longer bear any relationship to genome-wide genetic ancestry.

scholarly journals Autosomal admixture levels are informative about sex bias in admixed populations

2014 ◽  
Author(s):  
Amy Goldberg ◽  
Paul Verdu ◽  
Noah A Rosenberg
Keyword(s):  
Sex Chromosomes ◽  
Sex Bias ◽  
Source Population ◽  
Effective Population ◽  
History Of ◽  
Specific Source ◽  
Unequal Number ◽  
Admixed Population ◽  
Source Populations

AbstractSex-biased admixture has been observed in a wide variety of admixed populations. Genetic variation in sex chromosomes and ratios of quantities computed from sex chromosomes and autosomes have often been examined in order to infer patterns of sex-biased admixture, typically using statistical approaches that do not mechanistically model the complexity of a sex-specific history of admixture. Here, expanding on a model of Verdu & Rosenberg (2011) that did not include sex specificity, we develop a model that mechanistically examines sex-specific admixture histories. Under the model, multiple source populations contribute to an admixed population, potentially with their male and female contributions varying over time. In an admixed population descended from two source groups, we derive the moments of the distribution of the autosomal admixture fraction from a specific source population as a function of sex-specific introgression parameters and time. Considering admixture processes that are constant in time, we demonstrate that surprisingly, although the mean autosomal admixture fraction from a specific source population does not reveal a sex bias in the admixture history, the variance of autosomal admixture is informative about sex bias. Specifically, the long-term variance decreases as the sex bias from a contributing source population increases. This result can be viewed as analogous to the reduction in effective population size for populations with an unequal number of breeding males and females. Our approach can contribute to methods for inference of the history of complex sex-biased admixture processes by enabling consideration of the effect of sex-biased admixture on autosomal DNA.

Studying how genetic variants affect mechanism in biological systems

2018 ◽  
Vol 62 (4) ◽  
pp. 575-582
Author(s):  
Francesco Raimondi ◽  
Robert B. Russell
Keyword(s):  
Genetic Variation ◽  
Molecular Mechanism ◽  
Genetic Variants ◽  
Biological Function ◽  
Biological Systems ◽  
Protein Structures ◽  
Clinical Applications ◽  
Biological Pathways ◽  
The Relationship

Genetic variants are currently a major component of system-wide investigations into biological function or disease. Approaches to select variants (often out of thousands of candidates) that are responsible for a particular phenomenon have many clinical applications and can help illuminate differences between individuals. Selecting meaningful variants is greatly aided by integration with information about molecular mechanism, whether known from protein structures or interactions or biological pathways. In this review we discuss the nature of genetic variants, and recent studies highlighting what is currently known about the relationship between genetic variation, biomolecular function, and disease.

Growth Models with Corrections for the Retardative Effects of Tagging

1994 ◽  
Vol 51 (2) ◽  
pp. 263-267 ◽  
Author(s):  
Yongshun Xiao
Keyword(s):  
Growth Parameters ◽  
Growth Models ◽  
Simulated Data ◽  
Fish Growth ◽  
Lates Calcarifer ◽  
General Utility ◽  
Potential Applications ◽  
Length Increment ◽  
Animal Growth ◽  
Special Case

Length increment data from mark–recapture experiments are commonly used to obtain information on animal growth, assuming that tagging does not affect the growth of marked animals. The assumption is violated in many studies, but the effects of tagging on growth and estimates of growth parameters have not been and cannot be examined without appropriate models. This paper describes a model allowing quantification and estimation of the retarding effects of tagging on animal growth simultaneously with growth parameters in all existing growth models, reduction or elimination of biases in growth parameters induced by tagging, and relaxation of a key assumption in growth analysis using length increment data. A special case of this model was applied to simulated data and to tagging data from a centropomid perch (Lates calcarifer) to demonstrate its general utility. Tagging was inferred to have stopped the fish growth for 36.44 d (ASE = 12.70 d) if von Bertalanffy growth is assumed, but the period of recovery from tagging seemed size or age independent within the size range studied. If tagging retards animal growth, L∞ is slightly overestimated and K underestimated for unbiased data. Potential applications and limitations of the model are also discussed.

scholarly journals Aspectos nutricionais da variação genética em progênies de Myracrodruon urundeuva Fr. All. sob diferentes condições de cultivo

FLORESTA ◽  
1999 ◽  
Vol 29 (12) ◽  
Author(s):  
SIMONE APARECIDA DE OLIVEIRA ◽  
MARIO LUIZ TEIXEIRA DE MORAES ◽  
SALATIÉR BUZETTI
Keyword(s):  
Genetic Variation ◽  
Genetic Variability ◽  
Selection Process ◽  
Block Design ◽  
Nutrient Content ◽  
Open Pollination ◽  
Experimental Station ◽  
Old Trees

Sementes de aroeira foram obtidas a partir de 30 árvores de polinização livre, localizadas na Estação Ecológica do Instituto Florestal em Paulo de Faria - SP, em setembro de 1996. Foram instalados dois testes de progênies de aroeira (consorciado com mutambo e angico do campo – Exp 1 e homogêneo – Exp 2), em março de 1997, na Fazenda de Ensino e Pesquisa da FEIS/UNESP, em Selvíria - MS. O delineamento experimental utilizado foram os blocos casualizados, tanto no experimento consorciado como no homogêneo. Os caracteres nutricionais avaliados foram o conteúdo de: N, P, K, Ca, Mg e S. As estimativas de parâmetros genéticos foram obtidas em nível de média de parcelas. A herdabilidade, aos dois anos, variou de 0,05 (para o Mg) a 0,63 (para o N). Foi encontrada variabilidade genética para o teor de nutrientes e a característica mais indicada para um processo de seleção seria o conteúdo de N. Nutrient aspects of genetic variation on progeny of Myracrodruon urundeuva Fr. All. under different condition of crop Abstract Aroeira seeds were obtained from 30 trees of open pollination, located in the Estação Ecológica do Instituto Florestal in Paulo de Faria – SP, in September, 1996. Two tests of Aroeira progeny were conducted (mutambo and angico together – Exp 1 and homogeneous – Exp 2), in March, 1997, at experimental station of FEIS/UNESP, in Selvíria – MS. A randomized completely block design, to both experiments was used. The nutrient content evaluated was: N, P, K, Ca, Mg, and S. The genetic estimates achieved to mean plot level and herdability on 2 year old trees was 0,05 to Mg and 0,63 to N. There was genetic variability to nutrient content and N was the better characteristic to selection process.

scholarly journals Evaluating the genetic variability of rubber hybrid progenies of the two crosses PB260 x RO44/71 and PB260 x RO62/54 by RAPD technique

2019 ◽  
Vol 2 (3) ◽  
pp. 36-43
Author(s):  
Thien Minh Nguyen ◽  
Tien Thi My Pham
Keyword(s):  
Genetic Variation ◽  
Genetic Variability ◽  
Genetic Similarity ◽  
Field Experiments ◽  
Agronomic Traits ◽  
Genetic Relationships ◽  
Genetic Material ◽  
Population Based ◽  
Shannon Index ◽  
Polymorphic Bands

The agronomic values of this population have been evaluated in the field experiments based on their phenotypic performance of agronomic traits, but the genetic variability of this population needs to be evaluated via techniques based on genetic material - DNA. In this study, the genetic variability in the investigated population of 71 hybrids and their parents was evaluated by RAPD technique, using eight selected arbitrarily primers; Genetic parameters and dendrogram expressing the genetic relationships among the investigated population were analyzed by GenALEx 6.1, Popgene 1.31 and NTSYSpc 2.1 softwares. Eight primers were used to generate the amplify products on each individual in the investigated population. From 74 genotypes, a total of 109 fragments were generated, among which, there were 89 polymorphic bands representing 81.65% with an average of 11 polymorphic bands/primer. Genetic similarity coefficient among the investigated population, based on DICE coefficient, ranged from 0.560 (LH05/0822 and PB260) to 0.991 (LH05/0781 and LH05/0841) with an average of 0,796, meaning that the genetic distance among ranged from 0.009 to 0.440 with an average of 0.231. The Shannon index and mean heterozygosity values were 0.328 and 0,176, respectively. This indicated that the progenies of the two investigated crosses possessed a relatively high range of genetic variability. The analysis of molecular variance (AMOVA) showed that genetic variation within population represented 62%, while genetic variation among two different crosses contributes 38% to the total genetic variability. Dendrogram based on DICE’s genetic similarity using UPGMA method showed that the hybrids divide into two major genetic groups (0.75), but the crosses were scattered independently of the hybrid.

scholarly journals Estimating the timing of multiple admixture pulses during local ancestry inference

2018 ◽  
Author(s):  
Paloma Medina ◽  
Bryan Thornlow ◽  
Rasmus Nielsen ◽  
Russell Corbett-Detig
Keyword(s):  
Biological Process ◽  
Genetic Material ◽  
Simulated Data ◽  
Sub Saharan Africa ◽  
African Populations ◽  
Fundamental Biological Process ◽  
Admixed Population ◽  
Sub Saharan ◽  
Local Ancestry Inference ◽  
Admixture Event

ABSTRACTAdmixture, the mixing of genetically distinct populations, is increasingly recognized as a fundamental biological process. One major goal of admixture analyses is to estimate the timing of admixture events. Whereas most methods today can only detect the most recent admixture event, here we present coalescent theory and associated software that can be used to estimate the timing of multiple admixture events in an admixed population. We extensively validate this approach and evaluate the conditions under which it can succesfully distinguish one from two-pulse admixture models. We apply our approach to real and simulated data of Drosophila melanogaster. We find evidence of a single very recent pulse of cosmopolitan ancestry contributing to African populations as well as evidence for more ancient admixture among genetically differentiated populations in sub-Saharan Africa. These results suggest our method can quantify complex admixture histories involving genetic material introduced by multiple discrete admixture pulses. The new method facilitates the exploration of admixture and its contribution to adaptation, ecological divergence, and speciation.

scholarly journals The fog of genetics: Known unknowns and unknown unknowns in the genetics of complex traits and diseases

2019 ◽  
Author(s):  
João Pedro de Magalhães ◽  
Jingwei Wang
Keyword(s):  
Genetic Variability ◽  
Genetic Variants ◽  
Genetic Information ◽  
Complex Traits ◽  
Drug Targets ◽  
Molecular Mechanisms ◽  
Genetic Associations ◽  
Missing Heritability ◽  
Genome Space ◽  
Known Unknowns

AbstractAssociating genetic variants with phenotypes is not only important to understand the underlying biology but also to identify potential drug targets for treating diseases. It is widely accepted that for most complex traits many associations remain to be discovered, the so-called “missing heritability.” Yet missing heritability can be estimated, it is a known unknown, and we argue is only a fraction of the unknowns in genetics. The majority of possible genetic variants in the genome space are either too rare to be detected or even entirely absent from populations, and therefore do not contribute to estimates of phenotypic or genetic variability. We call these unknown unknowns in genetics the “fog of genetics.” Using data from the 1000 Genomes Project we then show that larger genes with greater genetic diversity are more likely to be associated with human traits, demonstrating that genetic associations are biased towards particular types of genes and that the genetic information we are lacking about traits and diseases is potentially immense. Our results and model have multiple implications for how genetic variability is perceived to influence complex traits, provide insights on molecular mechanisms of disease and for drug discovery efforts based on genetic information.

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