scholarly journals Bayesian Estimation of Population Size Changes by Sampling Tajima’s Trees

2019 ◽  
Author(s):  
Julia A. Palacios ◽  
Amandine Véber ◽  
Lorenzo Cappello ◽  
Zhangyuan Wang ◽  
John Wakeley ◽  
...  
Keyword(s):  
State Space ◽  
Bayesian Estimation ◽  
Population Size ◽  
Simulated Data ◽  
Effective Population ◽  
Large State Space ◽  
Population Sizes ◽  
Efficient Alternative ◽  
Inference Methods ◽  
Kingman’S Coalescent

AbstractThe large state space of gene genealogies is a major hurdle for inference methods based on Kingman’s coalescent. Here, we present a new Bayesian approach for inferring past population sizes which relies on a lower resolution coalescent process we refer to as “Tajima’s coalescent”. Tajima’s coalescent has a drastically smaller state space, and hence it is a computationally more efficient model, than the standard Kingman coalescent. We provide a new algorithm for efficient and exact likelihood calculations for data without recombination, which exploits a directed acyclic graph and a correspondingly tailored Markov Chain Monte Carlo method. We compare the performance of our Bayesian Estimation of population size changes by Sampling Tajima’s Trees (BESTT) with a popular implementation of coalescent-based inference in BEAST using simulated data and human data. We empirically demonstrate that BESTT can accurately infer effective population sizes, and it further provides an efficient alternative to the Kingman’s coalescent. The algorithms described here are implemented in the R package phylodyn, which is available for download at https://github.com/JuliaPalacios/phylodyn.

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 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 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 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.

scholarly journals On the estimation of ancestral population sizes of modern humans

1997 ◽  
Vol 69 (2) ◽  
pp. 111-116 ◽  
Author(s):  
ZIHENG YANG
Keyword(s):  
Population Size ◽  
Sequence Data ◽  
Divergence Time ◽  
Ancestral Population ◽  
Rate Variation ◽  
Effective Population ◽  
Modern Humans ◽  
Extant Species ◽  
Population Sizes ◽  
Highly Correlated

The theory developed by Takahata and colleagues for estimating the effective population size of ancestral species using homologous sequences from closely related extant species was extended to take account of variation of evolutionary rates among loci. Nuclear sequence data related to the evolution of modern humans were reanalysed and computer simulations were performed to examine the effect of rate variation on estimation of ancestral population sizes. It is found that the among-locus rate variation does not have a significant effect on estimation of the current population size when sequences from multiple loci are sampled from the same species, but does have a significant effect on estimation of the ancestral population size using sequences from different species. The effects of ancestral population size, species divergence time and among-locus rate variation are found to be highly correlated, and to achieve reliable estimates of the ancestral population size, effects of the other two factors should be estimated independently.

scholarly journals Repeatability of adaptation in experimental populations of different sizes

2015 ◽  
Vol 282 (1805) ◽  
pp. 20143033 ◽  
Author(s):  
Josianne Lachapelle ◽  
Joshua Reid ◽  
Nick Colegrave
Keyword(s):  
Population Size ◽  
Large Contribution ◽  
Unicellular Alga ◽  
Effective Population ◽  
Fitness Level ◽  
Relative Contribution ◽  
Large Populations ◽  
Population Sizes ◽  
Evolutionary Trajectories ◽  
Experimental Populations

The degree to which evolutionary trajectories and outcomes are repeatable across independent populations depends on the relative contribution of selection, chance and history. Population size has been shown theoretically and empirically to affect the amount of variation that arises among independent populations adapting to the same environment. Here, we measure the contribution of selection, chance and history in different-sized experimental populations of the unicellular alga Chlamydomonas reinhardtii adapting to a high salt environment to determine which component of evolution is affected by population size. We find that adaptation to salt is repeatable at the fitness level in medium ( N e = 5 × 10 4 ) and large ( N e = 4 × 10 5 ) populations because of the large contribution of selection. Adaptation is not repeatable in small ( N e = 5 × 10 3 ) populations because of large constraints from history. The threshold between stochastic and deterministic evolution in this case is therefore between effective population sizes of 10 3 and 10 4 . Our results indicate that diversity across populations is more likely to be maintained if they are small. Experimental outcomes in large populations are likely to be robust and can inform our predictions about outcomes in similar situations.

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.

scholarly journals A Simulation Study on Increasing Capture Periods in Bayesian Closed Population Capture-Recapture Models with Heterogeneity

2020 ◽  
Vol 18 (1) ◽  
pp. 2-23
Author(s):  
Ross M. Gosky ◽  
Joel Sanqui
Keyword(s):  
Population Size ◽  
Simulation Study ◽  
Simulated Data ◽  
Population Models ◽  
Data Set ◽  
Closed Population ◽  
Population Sizes ◽  
Capture Recapture

Capture-Recapture models are useful in estimating unknown population sizes. A common modeling challenge for closed population models involves modeling unequal animal catchability in each capture period, referred to as animal heterogeneity. Inference about population size N is dependent on the assumed distribution of animal capture probabilities in the population, and that different models can fit a data set equally well but provide contradictory inferences about N. Three common Bayesian Capture-Recapture heterogeneity models are studied with simulated data to study the prevalence of contradictory inferences is in different population sizes with relatively low capture probabilities, specifically at different numbers of capture periods in the study.

scholarly journals Joint Estimation of Pedigrees and Effective Population Size Using Markov Chain Monte Carlo

2018 ◽  
Author(s):  
Amy Ko ◽  
Rasmus Nielsen
Keyword(s):  
Monte Carlo ◽  
Markov Chain ◽  
Markov Chain Monte Carlo ◽  
Population Size ◽  
Effective Population Size ◽  
Simulated Data ◽  
Composite Likelihood ◽  
Joint Estimation ◽  
Pedigree Information ◽  
Effective Population

Pedigrees provide a fine resolution of the genealogical relationships among individuals and serve an important function in many areas of genetic studies. One such use of pedigree information is in the estimation of short-term effective population size (Ne), which is of great relevance in fields such as conservation genetics. Despite the usefulness of pedigrees, however, they are often an unknown parameter and must be inferred from genetic data. In this study, we present a Bayesian method to jointly estimate pedigrees and Ne from genetic markers using Markov Chain Monte Carlo. Our method supports analysis of a large number of markers and individuals with the use of composite likelihood, which significantly increases computational efficiency. We show on simulated data that our method is able to jointly estimate relationships up to first cousins and Ne with high accuracy. We also apply the method on a real dataset of house sparrows to reconstruct their previously unreported pedigree.

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