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 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 Introgression makes waves in inferred histories of effective population size

2017 ◽  
Author(s):  
John Hawks
Keyword(s):  
Gene Flow ◽  
Population Size ◽  
Effective Population Size ◽  
Population History ◽  
Human Populations ◽  
Effective Population ◽  
History Of ◽  
Or Gene ◽  
Time Of Origin ◽  
Past Population

AbstractHuman populations have a complex history of introgression and of changing population size. Human genetic variation has been affected by both these processes, so that inference of past population size depends upon the pattern of gene flow and introgression among past populations. One remarkable aspect of human population history as inferred from genetics is a consistent “wave” of larger effective population size, prior to the bottlenecks and expansions of the last 100,000 years. Here I carry out a series of simulations to investigate how introgression and gene flow from genetically divergent ancestral populations affect the inference of ancestral effective population size. Both introgression and gene flow from an extinct, genetically divergent population consistently produce a wave in the history of inferred effective population size. The time and amplitude of the wave reflect the time of origin of the genetically divergent ancestral populations and the strength of introgression or gene flow. These results demonstrate that even small fractions of introgression or gene flow from ancient populations may have large effects on the inference of effective population size.

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 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 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.

scholarly journals Coalescent models at small effective population sizes and population declines are positively misleading

2019 ◽  
Author(s):  
M. Elise Lauterbur
Keyword(s):  
Genetic Diversity ◽  
Sample Size ◽  
Population Size ◽  
Effective Population Size ◽  
Genetic Relationships ◽  
Population Decline ◽  
Population Declines ◽  
Effective Population ◽  
Analytical Approximations ◽  
Population Sizes

AbstractPopulation genetics employs two major models for conceptualizing genetic relationships among individuals – outcome-driven (coalescent) and process-driven (forward). These models are complementary, but the basic Kingman coalescent and its extensions make fundamental assumptions to allow analytical approximations: a constant effective population size much larger than the sample size. These make the probability of multiple coalescent events per generation negligible. Although these assumptions are often violated in species of conservation concern, conservation genetics often uses coalescent models of effective population sizes and trajectories in endangered species. Despite this, the effect of very small effective population sizes, and their interaction with bottlenecks and sample sizes, on such analyses of genetic diversity remains unexplored. Here, I use simulations to analyze the influence of small effective population size, population decline, and their relationship with sample size, on coalescent-based estimates of genetic diversity. Compared to forward process-based estimates, coalescent models significantly overestimate genetic diversity in oversampled populations with very small effective sizes. When sampled soon after a decline, coalescent models overestimate genetic diversity in small populations regardless of sample size. Such overestimates artificially inflate estimates of both bottleneck and population split times. For conservation applications with small effective population sizes, forward simulations that do not make population size assumptions are computationally tractable and should be considered instead of coalescent-based models. These findings underscore the importance of the theoretical basis of analytical techniques as applied to conservation questions.

scholarly journals Biodiversity Management Under Limiting Conditions: Estimating Effective Population Size Using the Molecular Mark and Recapture (MMR) Method

Sociobiology ◽  
2014 ◽  
Vol 59 (1) ◽  
pp. 165
Author(s):  
Kaori Murase ◽  
Masaharu Fukita
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
National Parks ◽  
Hot Spots ◽  
First Generation ◽  
Second Generation ◽  
Effective Population ◽  
Simple Method ◽  
Population Sizes ◽  
Virtual Species

Although many people have been paying attention to the decrease of biodiversity on earth in recent years, many local people, even staff of national parks, live under limiting conditions (such as a shortage of funds, specialists, literature, equipment for experiments and so on). To conserve biodiversity, it is important to be clear about which species decrease or increase. To find such information, it is quite important to know the dynamics of effective population size for each species. Although a large number of papers have been written about how to improve the precision of the estimated effective population size, little has been studied on how to estimate the dynamics of the effective population sizes for many species together under limiting situations, very similar to the management methods of national parks in countries which have biological hot spots. In this paper, we are not concerned with the improvement of the precision of the estimates. We do, however, propose a simple method for the estimation of the effective population size. We named it the “MMR method.” It is not difficult to understand and is easily applied to many species. To show the usefulness of the MMR method we made simple virtual species, which included the first generation and the second generation, on a computer, and then we conducted simulations to estimate the effective population size of the first generation. We calculated three statistics to estimate whether the MMR method is useful or not. The three statistics showed that the MMR method is useful.

Sign in / Sign up

Export Citation Format

Share Document