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.

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 When and how? Freshwater mussel recolonization in Lake Orta

2016 ◽  
Vol 75 (s2) ◽  
Author(s):  
Nicoletta Riccardi ◽  
Elsa Froufe ◽  
Manuel Lopes-Lima ◽  
Claudio Mazzoli
Keyword(s):  
Sediment Quality ◽  
Freshwater Mussel ◽  
Trophic Chain ◽  
Older Individuals ◽  
Host Fish ◽  
History Of ◽  
Water And Sediment Quality ◽  
Source Populations ◽  
Term Monitoring

Thanks to a video posted on a social network, live mussels of <em>Unio elongatulus</em>, have been recorded from Lake Orta (Italy) over one century after the last (and only) report. With its long and well documented history of pollution, Lake Orta offers the opportunity to document the post-extirpation recovery of freshwater unionid mussels. This case evidences that recovery/recolonization is possible despite a high devastation in the past, and permits to evaluate how fast recolonization may occur, in which way, and in what conditions.  The answer to the '<em>how</em> <em>fast</em>' was sought by estimating the age of the larger and seemingly older individuals of the population. To address the '<em>in which way</em>' we compared the haplotypes of Lake Orta specimens of <em>Unio elongatulus</em> (the only species present) with those of surrounding populations. We concluded that, since Lake Orta lacks a direct connection with the putative source populations, colonizing mussels were almost certainly transported by fish carrying glochidia that were used for lake restocking after liming. Data from the long-term monitoring of water chemistry and sediments have allowed defining what conditions proved to be suitable for survival making possible the start of mussels recovery. But not only water and sediment quality matters for mussels recovery, which was delayed by nearly ten years after the reappearance of fish. This delay reflects the need of the whole trophic chain to be reestablished to allow the survival of the suitable and healthy host-fish populations necessary for mussels reproduction.

scholarly journals Combining superior alleles from two homozygous populations in a cross-fertilizing species

1980 ◽  
Vol 36 (3) ◽  
pp. 277-287 ◽  
Author(s):  
Y. T. Ho ◽  
R. E. Comstock
Keyword(s):  
Real Life ◽  
The Other ◽  
Relative Fitness ◽  
Source Population ◽  
Effective Population ◽  
Complete Dominance ◽  
Selection Limit ◽  
The Difference ◽  
Source Populations ◽  
Foundation Stock

SUMMARYThe issue of incorporating the good alleles from two homozygous populations of a cross-fertilizing species into a single improved population was investigated assuming independent assortment, no epistasis, and either complete dominance (of the favourable or the unfavourable alleles) or additive genes. The selection limit in the foundation stock is a function of the effective population size (N), the proportion (x) contributed by the better source population (P1), the difference in relative fitness between single locus homozygotes and the proportion of loci (that will segregate in the foundation stock) fixed favourably in P1. In real life the last two of these are never known. We therefore focused on the response limits given x = 0·5, 0·75, 0·875 or the optimum value of x (which is a function of the other three parameters). Our general finding was that in situations where N is large enough so that a major portion of the potential can be achieved, the F2 population should be used as the foundation stock when the two source populations do not differ greatly in performance; but when one population performs considerably better than the other, the first backcross (but not second backcross) would be the choice.

scholarly journals Assessing the performance of qpAdm: a statistical tool for studying population admixture

Genetics ◽  
2021 ◽  
Author(s):  
Éadaoin Harney ◽  
Nick Patterson ◽  
David Reich ◽  
John Wakeley
Keyword(s):  
Best Practices ◽  
Relative Proportion ◽  
Population History ◽  
Source Population ◽  
Population Admixture ◽  
Single Model ◽  
Statistical Tool ◽  
History Of ◽  
Data Coverage ◽  
Source Populations

Abstract qpAdm is a statistical tool for studying the ancestry of populations with histories that involve admixture between two or more source populations. Using qpAdm, it is possible to identify plausible models of admixture that fit the population history of a group of interest and to calculate the relative proportion of ancestry that can be ascribed to each source population in the model. Although qpAdm is widely used in studies of population history of human (and nonhuman) groups, relatively little has been done to assess its performance. We performed a simulation study to assess the behavior of qpAdm under various scenarios in order to identify areas of potential weakness and establish recommended best practices for use. We find that qpAdm is a robust tool that yields accurate results in many cases, including when data coverage is low, there are high rates of missing data or ancient DNA damage, or when diploid calls cannot be made. However, we caution against co-analyzing ancient and present-day data, the inclusion of an extremely large number of reference populations in a single model, and analyzing population histories involving extended periods of gene flow. We provide a user guide suggesting best practices for the use of qpAdm.

scholarly journals Estimation of Long-Term Effective Population Sizes Through the History of Durum Wheat Using Microsatellite Data

Genetics ◽  
2004 ◽  
Vol 169 (3) ◽  
pp. 1589-1599 ◽  
Author(s):  
A.-C. Thuillet ◽  
T. Bataillon ◽  
S. Poirier ◽  
S. Santoni ◽  
J. L. David
Keyword(s):  
Durum Wheat ◽  
Microsatellite Data ◽  
Effective Population ◽  
Population Sizes ◽  
History Of

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 Faunal record identifies Bering isthmus conditions as constraint to end-Pleistocene migration to the New World

2014 ◽  
Vol 281 (1776) ◽  
pp. 20132167 ◽  
Author(s):  
Meirav Meiri ◽  
Adrian M. Lister ◽  
Matthew J. Collins ◽  
Noreen Tuross ◽  
Ted Goebel ◽  
...  
Keyword(s):  
Ancient Dna ◽  
Cervus Elaphus ◽  
New World ◽  
Modern Human ◽  
Source Population ◽  
14C Dating ◽  
The North ◽  
History Of ◽  
Human Colonization

Human colonization of the New World is generally believed to have entailed migrations from Siberia across the Bering isthmus. However, the limited archaeological record of these migrations means that details of the timing, cause and rate remain cryptic. Here, we have used a combination of ancient DNA, 14C dating, hydrogen and oxygen isotopes, and collagen sequencing to explore the colonization history of one of the few other large mammals to have successfully migrated into the Americas at this time: the North American elk ( Cervus elaphus canadensis ), also known as wapiti. We identify a long-term occupation of northeast Siberia, far beyond the species’s current Old World distribution. Migration into North America occurred at the end of the last glaciation, while the northeast Siberian source population became extinct only within the last 500 years. This finding is congruent with a similar proposed delay in human colonization, inferred from modern human mitochondrial DNA, and suggestions that the Bering isthmus was not traversable during parts of the Late Pleistocene. Our data imply a fundamental constraint in crossing Beringia, placing limits on the age and mode of human settlement in the Americas, and further establish the utility of ancient DNA in palaeontological investigations of species histories.

Karyotypic Evolution and Long-Term Effective Population Sizes of Birds

The Auk ◽  
1984 ◽  
Vol 101 (1) ◽  
pp. 99-102 ◽  
Author(s):  
George F. Barrowclough ◽  
Gerald F. Shields
Keyword(s):  
Geographic Variation ◽  
Karyotypic Evolution ◽  
Effective Population ◽  
Allelic Frequencies ◽  
Demographic Modeling ◽  
Population Sizes ◽  
History Of ◽  
Karyotypic Change ◽  
Wide Assortment

Abstract Rates of karyotypic change in birds are used to estimate that, over the longterm history of a wide assortment of genera, avian effective population sizes have averaged on the order of 100. This result is consistent with the results of electrophoretic studies of geographic variation of allelic frequencies within species but is somewhat less consistent with the results obtained from demographic modeling. Three methodologically independent analyses have now corroborated the hypothesis that avian effective population sizes are typically of the order of 102 or larger.

scholarly journals Assessing the Performance of qpAdm: A Statistical Tool for Studying Population Admixture

2020 ◽  
Author(s):  
Éadaoin Harney ◽  
Nick Patterson ◽  
David Reich ◽  
John Wakeley
Keyword(s):  
Best Practices ◽  
Relative Proportion ◽  
Population History ◽  
Source Population ◽  
Population Admixture ◽  
Single Model ◽  
Statistical Tool ◽  
History Of ◽  
Data Coverage ◽  
Source Populations

ABSTRACTqpAdm is a statistical tool for studying the ancestry of populations with histories that involve admixture between two or more source populations. Using qpAdm, it is possible to identify plausible models of admixture that fit the population history of a group of interest and to calculate the relative proportion of ancestry that can be ascribed to each source population in the model. Although qpAdm is widely used in studies of population history of human (and non-human) groups, relatively little has been done to assess its performance. We performed a simulation study to assess the behavior of qpAdm under various scenarios in order to identify areas of potential weakness and establish recommended best practices for use. We find that qpAdm is a robust tool that yields accurate results in many cases, including when data coverage is low, there are high rates of missing data or ancient DNA damage, or when diploid calls cannot be made. However, we caution against co-analyzing ancient and present-day data, the inclusion of an extremely large number of reference populations in a single model, and analyzing population histories involving extended periods of gene flow. We provide a user guide suggesting best practices for the use of qpAdm.

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