scholarly journals Transition densities and sample frequency spectra of diffusion processes with selection and variable population size

2015 ◽  
Author(s):  
Daniel Zivkovic ◽  
Matthias Steinrücken ◽  
Yun S. Song ◽  
Wolfgang Stephan
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Diffusion Processes ◽  
Transition Density ◽  
Effective Population ◽  
Frequency Spectra ◽  
Transition Densities ◽  
Population Sizes ◽  
Sample Frequency ◽  
The Impact

Advances in empirical population genetics have made apparent the need for models that simultaneously account for selection and demography. To address this need, we here study the Wright-Fisher diffusion under selection and variable effective population size. In the case of genic selection and piecewise-constant effective population sizes, we obtain the transition density function by extending a recently developed method for computing an accurate spectral representation for a constant population size. Utilizing this extension, we show how to compute the sample frequency spectrum (SFS) in the presence of genic selection and an arbitrary number of instantaneous changes in the effective population size. We also develop an alternate, efficient algorithm for computing the SFS using a method of moments. We apply these methods to answer the following questions: If neutrality is incorrectly assumed when there is selection, what effects does it have on demographic parameter estimation? Can the impact of negative selection be observed in populations that undergo strong exponential growth?

scholarly journals SpectralTDF: transition densities of diffusion processes with time-varying selection parameters, mutation rates, and effective population sizes

2015 ◽  
Author(s):  
Matthias Steinrücken ◽  
Ethan M Jewett ◽  
Yun S Song
Keyword(s):  
Spectral Representation ◽  
Diffusion Processes ◽  
Transition Density ◽  
Effective Population ◽  
Piecewise Constant ◽  
Practical Applications ◽  
Transition Density Function ◽  
Transition Densities ◽  
Population Sizes ◽  
Selection Parameters

In the Wright-Fisher diffusion, the transition density function (TDF) describes the time-evolution of the population-wide frequency of an allele. This function has several practical applications in population genetics, and computing it for biologically realistic scenarios with selection and demography is an important problem. We develop an efficient method for finding a spectral representation of the TDF for a general model where the effective population size, selection coefficients, and mutation parameters vary over time in a piecewise constant manner. The method, called SpectralTDF, is available at https://sourceforge.net/projects/spectraltdf/.

scholarly journals Fluctuating fortunes: genomes and habitat reconstructions reveal global climate-mediated changes in bats' genetic diversity

2019 ◽  
Vol 286 (1911) ◽  
pp. 20190304 ◽  
Author(s):  
Balaji Chattopadhyay ◽  
Kritika M. Garg ◽  
Rajasri Ray ◽  
Frank E. Rheindt
Keyword(s):  
Climate Change ◽  
Genetic Diversity ◽  
Population Size ◽  
Effective Population Size ◽  
Global Climate ◽  
Future Climate Change ◽  
Effective Population ◽  
Population Sizes ◽  
Earth’S Climate ◽  
The Impact

Over the last approximately 2.6 Myr, Earth's climate has been dominated by cyclical ice ages that have profoundly affected species' population sizes, but the impact of impending anthropogenic climate change on species’ extinction potential remains a worrying problem. We investigated 11 bat species from different taxonomic, ecological and geographical backgrounds using combined information from palaeoclimatic habitat reconstructions and genomes to analyse biotic impacts of historic climate change. We discover tightly correlated fluctuations between species' historic distribution and effective population size, identify frugivores as particularly susceptible to global warming, pinpoint large insectivores as having overall low effective population size and flag the onset of the Holocene (approx. 10–12 000 years ago) as the period with the generally lowest effective population sizes across the last approximately 1 Myr. Our study shows that combining genomic and palaeoclimatological approaches reveals effects of climatic shifts on genetic diversity and may help predict impacts of future climate change.

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 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 NEW METHOD FOR ESTIMATING THE EFFECTIVE POPULATION SIZE FROM ALLELE FREQUENCY CHANGES

Genetics ◽  
1983 ◽  
Vol 104 (3) ◽  
pp. 531-548
Author(s):  
Edward Pollak
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Allele Frequency ◽  
New Method ◽  
Standard Errors ◽  
Effective Population ◽  
Census Size ◽  
Population Sizes ◽  
Frequency Changes ◽  
Approximate Expressions

ABSTRACT A new procedure is proposed for estimating the effective population size, given that information is available on changes in frequencies of the alleles at one or more independently segregating loci and the population is observed at two or more separate times. Approximate expressions are obtained for the variances of the new statistic, as well as others, also based on allele frequency changes, that have been discussed in the literature. This analysis indicates that the new statistic will generally have a smaller variance than the others. Estimates of effective population sizes and of the standard errors of the estimates are computed for data on two fly populations that have been discussed in earlier papers. In both cases, there is evidence that the effective population size is very much smaller than the minimum census size of the population.

The broad-snouted caiman population recovery in Argentina. A case of genetics conservation

2017 ◽  
Vol 38 (4) ◽  
pp. 411-424 ◽  
Author(s):  
Patricia Susana Amavet ◽  
Eva Carolina Rueda ◽  
Juan César Vilardi ◽  
Pablo Siroski ◽  
Alejandro Larriera ◽  
...  
Keyword(s):  
Genetic Variability ◽  
Population Size ◽  
Effective Population Size ◽  
Population Genetic ◽  
Genetic Parameters ◽  
Population Recovery ◽  
Santa Fe ◽  
Effective Population ◽  
Population Genetic Parameters ◽  
The Impact

Caiman latirostriswild populations have suffered a drastic reduction in the past, and for that reason, a management and monitoring plan was applied since 1990 in Santa Fe, Argentina in order to achieve population recovery. Although ranching system has a noteworthy success in terms of population size recovering, there is no information about the estimation of population genetic parameters. In particular, the consequence of the bottleneck underwent by these populations has not been assessed. We evaluated variability and genetic structure ofC. latirostrispopulations from Santa Fe through time, using microsatellites and mitochondrial DNA. Population genetic parameters were compared among four sites and three different periods to assess the impact of management activities, and effective population size was estimated in order to detect bottleneck events. We observed an increase in microsatellite variability and low genetic variability in mitochondrial lineages through time. Variability estimates are similar among sites in each sampling period; and there is scarce differentiation among them. The genetic background of each sampling site has changed through time; we assume this fact may be due to entry of individuals of different origin, through management and repopulation activities. Moreover, taking into account the expected heterozygosity and effective population size values, it can be assumed that bottleneck events indeed have occurred in the recent past. Our results suggest that, in addition to increasing population size, genetic variability of the species has been maintained. However, the information is still incomplete, and regular monitoring should continue in order to arrive to solid conclusions.

scholarly journals SNP-based analysis reveals unexpected features of genetic diversity, parental contributions and pollen contamination in a white spruce breeding program

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Esteban Galeano ◽  
Jean Bousquet ◽  
Barb R. Thomas
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Effective Population Size ◽  
White Spruce ◽  
Seed Orchard ◽  
Pedigree Reconstruction ◽  
Effective Population ◽  
Pollen Contamination ◽  
Contamination Levels ◽  
The Impact

AbstractAccurate monitoring of genetic diversity levels of seedlots and mating patterns of parents from seed orchards are crucial to ensure that tree breeding programs are long-lasting and will deliver anticipated genetic gains. We used SNP genotyping to characterize founder trees, five bulk seed orchard seedlots, and trees from progeny trials to assess pollen contamination and the impact of severe roguing on genetic diversity and parental contributions in a first-generation open-pollinated white spruce clonal seed orchard. After severe roguing (eliminating 65% of the seed orchard trees), we found a slight reduction in the Shannon Index and a slightly negative inbreeding coefficient, but a sharp decrease in effective population size (eightfold) concomitant with sharp increase in coancestry (eightfold). Pedigree reconstruction showed unequal parental contributions across years with pollen contamination levels between 12 and 51% (average 27%) among seedlots, and 7–68% (average 30%) among individual genotypes within a seedlot. These contamination levels were not correlated with estimates obtained using pollen flight traps. Levels of pollen contamination also showed a Pearson’s correlation of 0.92 with wind direction, likely from a pollen source 1 km away from the orchard under study. The achievement of 5% genetic gain in height at rotation through eliminating two-thirds of the orchard thus generated a loss in genetic diversity as determined by the reduction in effective population size. The use of genomic profiles revealed the considerable impact of roguing on genetic diversity, and pedigree reconstruction of full-sib families showed the unanticipated impact of pollen contamination from a previously unconsidered source.

Estimating Ancestral Population Sizes and Divergence Times

Genetics ◽  
2003 ◽  
Vol 163 (1) ◽  
pp. 395-404 ◽  
Author(s):  
Jeffrey D Wall
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Sequence Data ◽  
Ancestral Population ◽  
Divergence Times ◽  
Intragenic Recombination ◽  
Intergenic Sequence ◽  
Effective Population ◽  
Recombination Rates ◽  
Population Sizes

Abstract This article presents a new method for jointly estimating species divergence times and ancestral population sizes. The method improves on previous ones by explicitly incorporating intragenic recombination, by utilizing orthologous sequence data from closely related species, and by using a maximum-likelihood framework. The latter allows for efficient use of the available information and provides a way of assessing how much confidence we should place in the estimates. I apply the method to recently collected intergenic sequence data from humans and the great apes. The results suggest that the human-chimpanzee ancestral population size was four to seven times larger than the current human effective population size and that the current human effective population size is slightly >10,000. These estimates are similar to previous ones, and they appear relatively insensitive to assumptions about the recombination rates or mutation rates across loci.

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