scholarly journals Changes in life history and population size can explain relative neutral diversity levels on X and autosomes in extant human populations

2019 ◽  
Author(s):  
Guy Amster ◽  
David A. Murphy ◽  
William M. Milligan ◽  
Guy Sella
Keyword(s):  
Life History ◽  
Population Size ◽  
Mutation Rates ◽  
Human Populations ◽  
Effective Population ◽  
Mutation Bias ◽  
Historical Changes ◽  
Generation Times ◽  
Population Sizes ◽  
Male Mutation Bias

AbstractIn human populations, relative levels of neutral polymorphism on the X and autosomes differ markedly from each other and from the naive theoretical expectation of ¾. These differences have attracted considerable attention, with studies highlighting several potential causes, including male biased mutation and reproductive variance, historical changes in population size, and selection at linked loci. We revisit this question in light of our new theory about the effects of life history and given pedigree-based estimates of the dependence of human mutation rates on sex and age. We demonstrate that life history effects, particularly higher generation times in males than females, likely had multiple effects on human X-to-autosomes (X:A) polymorphism ratios, through the extent of male mutation bias, the equilibrium X:A ratios of effective population sizes, and differential responses to changes in population size. We also show that the standard approach of using divergence between species to correct for the male bias in mutation results in biased estimates of X:A effective population size ratios. We obtain alternative estimates using pedigree-based estimates of the male mutation bias, which reveal X:A ratios of effective population sizes to be considerably greater than previously appreciated. We then show that the joint effects of historical changes in life history and population size can explain X:A polymorphism ratios in extant human populations. Our results suggest that ancestral human populations were highly polygynous; that non-African populations experienced a substantial reduction in polygyny and/or increase in male-biased generation times around the out of Africa bottleneck; and that extant diversity levels were affected by fairly recent changes in sex-specific life history.Significance StatementAll else being equal, the ratio of diversity levels on X and autosomes at selectively neutral sites should mirror the ratio of their numbers in the population and thus equal ¾. In reality, the ratios observed across human populations differ markedly from ¾ and from each other. Because from a population perspective, autosomes spend an equal number of generations in both sexes while the X spends twice as many generations in females, these departures from the naïve expectations likely reflect differences between male and female life histories and their effects on mutation processes. Indeed, we show that the ratios observed across human populations can be explained by demographic history, assuming plausible, sex-specific mutation rates, generation times and reproductive variances.

scholarly journals Changes in life history and population size can explain the relative neutral diversity levels on X and autosomes in extant human populations

2020 ◽  
Vol 117 (33) ◽  
pp. 20063-20069
Author(s):  
Guy Amster ◽  
David A. Murphy ◽  
William R. Milligan ◽  
Guy Sella
Keyword(s):  
Life History ◽  
Population Size ◽  
Mutation Rates ◽  
Human Populations ◽  
Effective Population ◽  
Mutation Bias ◽  
Female Ratio ◽  
Generation Times ◽  
Population Sizes ◽  
Male Mutation Bias

In human populations, the relative levels of neutral diversity on the X and autosomes differ markedly from each other and from the naïve theoretical expectation of 3/4. Here we propose an explanation for these differences based on new theory about the effects of sex-specific life history and given pedigree-based estimates of the dependence of human mutation rates on sex and age. We demonstrate that life history effects, particularly longer generation times in males than in females, are expected to have had multiple effects on human X-to-autosome (X:A) diversity ratios, as a result of male-biased mutation rates, the equilibrium X:A ratio of effective population sizes, and the differential responses to changes in population size. We also show that the standard approach of using divergence between species to correct for male mutation bias results in biased estimates of X:A effective population size ratios. We obtain alternative estimates using pedigree-based estimates of the male mutation bias, which reveal that X:A ratios of effective population sizes are considerably greater than previously appreciated. Finally, we find that the joint effects of historical changes in life history and population size can explain the observed X:A diversity ratios in extant human populations. Our results suggest that ancestral human populations were highly polygynous, that non-African populations experienced a substantial reduction in polygyny and/or increase in the male-to-female ratio of generation times around the Out-of-Africa bottleneck, and that current diversity levels were affected by fairly recent changes in sex-specific life history.

scholarly journals Human paternal and maternal demographic histories: insights from high-resolution Y chromosome and mtDNA sequences

2014 ◽  
Author(s):  
Sebastian Lippold ◽  
Hongyang Xu ◽  
Albert Ko ◽  
Mingkun Li ◽  
Gabriel Renaud ◽  
...  
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Y Chromosome ◽  
Global Scale ◽  
Human Populations ◽  
Effective Population ◽  
Population Sizes ◽  
History Of ◽  
Out Of Africa ◽  
Complete Mtdna

To investigate in detail the paternal and maternal demographic histories of humans, we obtained ~500 kb of non-recombining Y chromosome (NRY) sequences and complete mtDNA genome sequences from 623 males from 51 populations in the CEPH Human Genome Diversity Panel (HGDP). Our results: confirm the controversial assertion that genetic differences between human populations on a global scale are bigger for the NRY than for mtDNA; suggest very small ancestral effective population sizes (<100) for the out-of-Africa migration as well as for many human populations; and indicate that the ratio of female effective population size to male effective population size (Nf/Nm) has been greater than one throughout the history of modern humans, and has recently increased due to faster growth in Nf. However, we also find substantial differences in patterns of mtDNA vs. NRY variation in different regional groups; thus, global patterns of variation are not necessarily representative of specific geographic regions.

scholarly journals Alu Evolution in Human Populations: Using the Coalescent to Estimate Effective Population Size

Genetics ◽  
1997 ◽  
Vol 147 (4) ◽  
pp. 1977-1982
Author(s):  
Stephen T Sherry ◽  
Henry C Harpending ◽  
Mark A Batzer ◽  
Mark Stoneking
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Genomic Library ◽  
Diploid Cell ◽  
Human Populations ◽  
Effective Population ◽  
Alu Repeats ◽  
Branch Lengths ◽  
Diploid Cell Line ◽  
Coalescence Theory

Abstract There are estimated to be ~1000 members of the Ya5 Alu subfamily of retroposons in humans. This Subfamily has a distribution restricted to humans, with a few copies in gorillas and chimpanzees. Fifty-seven Ya5 elements were previously cloned from a HeLaderived randomly sheared total genomic library, sequenced, and screened for polymorphism in a panel of 120 unrelated humans. Forty-four of the 57 cloned Alu repeats were monomorphic in the sample and 13 Alu repeats were dimorphic for insertion presence/absence. The observed distribution of sample frequencies of the 13 dimorphic elements is consistent with the theoretical expectation for elements ascertained in a single diploid cell line. Coalescence theory is used to compute expected total pedigree branch lengths for monomorphic and dimorphic elements, leading to an estimate of human effective population size of ~18,000 during the last one to two million years.

scholarly journals EFFECTS OF POPULATION SIZE AND SELECTION INTENSITY ON SHORT-TERM RESPONSE TO SELECTION FOR POSTWEANING GAIN IN MICE

Genetics ◽  
1973 ◽  
Vol 73 (3) ◽  
pp. 513-530
Author(s):  
J P Hanrahan ◽  
E J Eisen ◽  
J E Legates
Keyword(s):  
Population Size ◽  
Selection Response ◽  
Selection Intensity ◽  
Realized Heritability ◽  
Family Selection ◽  
Effective Population ◽  
Population Sizes ◽  
Selection For ◽  
Selection Intensities ◽  
Term Response

ABSTRACT The effects of population size and selection intensity on the mean response was examined after 14 generations of within full-sib family selection for postweaning gain in mice. Population sizes of 1, 2, 4, 8 and 16 pair matings were each evaluated at selection intensities of 100% (control), 50% and 25% in a replicated experiment. Selection response per generation increased as selection intensity increased. Selection response and realized heritability tended to increase with increasing population size. Replicate variability in realized heritability was large at population sizes of 1, 2 and 4 pairs. Genetic drift was implicated as the primary factor causing the reduced response and lowered repeatability at the smaller population sizes. Lines with intended effective population sizes of 62 yielded larger selection responses per unit selection differential than lines with effective population sizes of 30 or less.

scholarly journals The effect of life-history and mode of inheritance on neutral genetic variability

2001 ◽  
Vol 77 (2) ◽  
pp. 153-166 ◽  
Author(s):  
BRIAN CHARLESWORTH
Keyword(s):  
Sequence Variation ◽  
Adult Mortality ◽  
Structured Populations ◽  
Human Populations ◽  
Effective Population ◽  
Transmission Modes ◽  
Population Sizes ◽  
Age Structured ◽  
Infinite Sites Model ◽  
Site Diversity

Formulae for the effective population sizes of autosomal, X-linked, Y-linked and maternally transmitted loci in age-structured populations are developed. The approximations used here predict both asymptotic rates of increase in probabilities of identity, and equilibrium levels of neutral nucleotide site diversity under the infinite-sites model. The applications of the results to the interpretation of data on DNA sequence variation in Drosophila, plant, and human populations are discussed. It is concluded that sex differences in demographic parameters such as adult mortality rates generally have small effects on the relative effective population sizes of loci with different modes of inheritance, whereas differences between the sexes in variance in reproductive success can have major effects, either increasing or reducing the effective population size for X-linked loci relative to autosomal or Y-linked loci. These effects need to be accounted for when trying to understand data on patterns of sequence variation for genes with different transmission modes.

scholarly journals Genetic diversity, demographic history and neo-sex chromosomes in the Critically Endangered Raso lark

2020 ◽  
Vol 287 (1922) ◽  
pp. 20192613 ◽  
Author(s):  
Elisa G. Dierickx ◽  
Simon Yung Wa Sin ◽  
H. Pieter J. van Veelen ◽  
M. de L. Brooke ◽  
Yang Liu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Sex Chromosomes ◽  
Demographic History ◽  
Large Population ◽  
Effective Population ◽  
Island Species ◽  
Population Sizes ◽  
Approaches To Study ◽  
Genetic Signatures

Small effective population sizes could expose island species to inbreeding and loss of genetic variation. Here, we investigate factors shaping genetic diversity in the Raso lark, which has been restricted to a single islet for approximately 500 years, with a population size of a few hundred. We assembled a reference genome for the related Eurasian skylark and then assessed diversity and demographic history using RAD-seq data (75 samples from Raso larks and two related mainland species). We first identify broad tracts of suppressed recombination in females, indicating enlarged neo-sex chromosomes. We then show that genetic diversity across autosomes in the Raso lark is lower than in its mainland relatives, but inconsistent with long-term persistence at its current population size. Finally, we find that genetic signatures of the recent population contraction are overshadowed by an ancient expansion and persistence of a very large population until the human settlement of Cape Verde. Our findings show how genome-wide approaches to study endangered species can help avoid confounding effects of genome architecture on diversity estimates, and how present-day diversity can be shaped by ancient demographic events.

scholarly journals Recombination Gives a New Insight in the Effective Population Size and the History of the Old World Human Populations

2011 ◽  
Vol 29 (1) ◽  
pp. 25-30 ◽  
Author(s):  
Marta Melé ◽  
Asif Javed ◽  
Marc Pybus ◽  
Pierre Zalloua ◽  
Marc Haber ◽  
...  
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Human Populations ◽  
Effective Population ◽  
Old World ◽  
History Of

scholarly journals Effective population size of current human population

2011 ◽  
Vol 93 (2) ◽  
pp. 105-114 ◽  
Author(s):  
LEEYOUNG PARK
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Human Population ◽  
Random Mating ◽  
Phase Iii ◽  
Human Populations ◽  
Effective Population ◽  
Hapmap Phase ◽  
Hardy Weinberg Equilibrium ◽  
Genetic Drifts

SummaryIn order to estimate the effective population size (Ne) of the current human population, two new approaches, which were derived from previous methods, were used in this study. One is based on the deviation from linkage equilibrium (LE) between completely unlinked loci in different chromosomes and another is based on the deviation from the Hardy–Weinberg Equilibrium (HWE). When random mating in a population is assumed, genetic drifts in population naturally induce linkage disequilibrium (LD) between chromosomes and the deviation from HWE. The latter provides information on the Ne of the current population, and the former provides the same when the Ne is constant. If Ne fluctuates, recent Ne changes are reflected in the estimates based on LE, and the comparison between two estimates can provide information regarding recent changes of Ne. Using HapMap Phase III data, the estimates were varied from 622 to 10 437, depending on populations and estimates. The Ne appeared to fluctuate as it provided different estimates for each of the two methods. These Ne estimates were found to agree approximately with the overall increment observed in recent human populations.

scholarly journals Mitochondrial DNA Sequence Diversity in Mammals: A Correlation between the Effective and Census Population Sizes

2020 ◽  
Vol 12 (12) ◽  
pp. 2441-2449
Author(s):  
Jennifer James ◽  
Adam Eyre-Walker
Keyword(s):  
Mitochondrial Dna ◽  
Metabolic Rate ◽  
Population Size ◽  
Effective Population Size ◽  
Dna Sequence ◽  
Range Size ◽  
Effective Population ◽  
Population Sizes ◽  
Census Population Size ◽  
The Relationship

Abstract What determines the level of genetic diversity of a species remains one of the enduring problems of population genetics. Because neutral diversity depends upon the product of the effective population size and mutation rate, there is an expectation that diversity should be correlated to measures of census population size. This correlation is often observed for nuclear but not for mitochondrial DNA. Here, we revisit the question of whether mitochondrial DNA sequence diversity is correlated to census population size by compiling the largest data set to date, using 639 mammalian species. In a multiple regression, we find that nucleotide diversity is significantly correlated to both range size and mass-specific metabolic rate, but not a variety of other factors. We also find that a measure of the effective population size, the ratio of nonsynonymous to synonymous diversity, is also significantly negatively correlated to both range size and mass-specific metabolic rate. These results together suggest that species with larger ranges have larger effective population sizes. The slope of the relationship between diversity and range is such that doubling the range increases diversity by 12–20%, providing one of the first quantifications of the relationship between diversity and the census population size.

Examination of the relationship between inbreeding and population size

1985 ◽  
Vol 17 (1) ◽  
pp. 97-106 ◽  
Author(s):  
John H. Relethford
Keyword(s):  
Population Structure ◽  
Linear Regression ◽  
Population Size ◽  
Effective Population Size ◽  
Linear Regression Model ◽  
Historical Change ◽  
Human Populations ◽  
Effective Population ◽  
The Common ◽  
The Relationship

SummaryA method is presented for examining the relationship between effective population size and accumulated random inbreeding in human populations. For a set of populations, the inverse of inbreeding is regressed on effective population size using a linear regression model. This procedure allows testing of several hypotheses regarding the common and unique influences on population structure. Deviations from the expected curve suggest demographic or historical change. This method is applied to surname data from nine Irish isolates. The results show that the method is very useful in assessing differential influences on population structure.

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