scholarly journals Effective population size/adult population size ratios in wildlife: a review

1995 ◽  
Vol 66 (2) ◽  
pp. 95-107 ◽  
Author(s):  
Richard Frankham
Keyword(s):  
Sex Ratio ◽  
Population Size ◽  
Effective Population Size ◽  
Family Size ◽  
Adult Population ◽  
Effective Population ◽  
Total Size ◽  
Relevant Variables ◽  
Population Sizes ◽  
Census Population Size

SummaryThe effective population size is required to predict the rate of inbreeding and loss of genetic variation in wildlife. Since only census population size is normally available, it is critical to know the ratio of effective to actual population size (Ne/N). Published estimates ofNe/N(192 from 102 species) were analysed to identify major variables affecting the ratio, and to obtain a comprehensive estimate of the ratio with all relevant variables included. The five most important variables explaining variation among estimates, in order of importance, were fluctuation in population size, variance in family size, form ofNused (adults υ. breeders υ. total size), taxonomic group and unequal sex-ratio. There were no significant effects on the ratio of high υ. low fecundity, demographic υ. genetic methods of estimation, or of overlapping υ. non-overlapping generations when the same variables were included in estimates. Comprehensive estimates ofNe/N(that included the effects of fluctuation in population size, variance in family size and unequal sex-ratio) averaged only 0·10–0·11. Wildlife populations have much smaller effective population sizes than previously recognized.

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 Mitochondrial DNA Sequence Diversity in Mammals: a Correlation Between the Effective and Census Population Sizes

2020 ◽  
Author(s):  
Jennifer James ◽  
Adam Eyre-Walker
Keyword(s):  
Mitochondrial Dna ◽  
Metabolic Rate ◽  
Population Size ◽  
Effective Population Size ◽  
Dna Sequence ◽  
Sequence Diversity ◽  
Effective Population ◽  
Population Sizes ◽  
Census Population Size ◽  
The Relationship

AbstractWhat determines the level of genetic diversity of a species remains one of the enduring problems of population genetics. Since, 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 dataset to date from 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 non-synonymous to synonymous diversity, is also significantly negatively correlated to both range 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 to 20%, providing one of the first quantifications of the relationship between effective and census population sizes.

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 Effective size of nonrandom mating populations.

Genetics ◽  
1992 ◽  
Vol 130 (4) ◽  
pp. 909-916 ◽  
Author(s):  
A Caballero ◽  
W G Hill
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Family Size ◽  
Genetic Drift ◽  
Effective Size ◽  
Effective Population ◽  
Gene Frequencies ◽  
Nonrandom Mating ◽  
Sib Mating ◽  
Census Number

Abstract Nonrandom mating whereby parents are related is expected to cause a reduction in effective population size because their gene frequencies are correlated and this will increase the genetic drift. The published equation for the variance effective size, Ne, which includes the possibility of nonrandom mating, does not take into account such a correlation, however. Further, previous equations to predict effective sizes in populations with partial sib mating are shown to be different, but also incorrect. In this paper, a corrected form of these equations is derived and checked by stochastic simulation. For the case of stable census number, N, and equal progeny distributions for each sex, the equation is [formula: see text], where Sk2 is the variance of family size and alpha is the departure from Hardy-Weinberg proportions. For a Poisson distribution of family size (Sk2 = 2), it reduces to Ne = N/(1 + alpha), as when inbreeding is due to selfing. When nonrandom mating occurs because there is a specified system of partial inbreeding every generation, alpha can be substituted by Wright's FIS statistic, to give the effective size as a function of the proportion of inbred mates.

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.

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.

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 Effective population size of an offshore population of bottlenose dolphins, Tursiops truncatus, from the São Pedro and São Paulo Archipelago, Brazil

10.5597/00225 ◽  
2017 ◽  
Vol 11 (1-2) ◽  
pp. 162-169 ◽  
Author(s):  
Larissa R. Oliveira ◽  
Paulo Henrique Ott ◽  
Ignacio B. Moreno ◽  
Maurício Tavares ◽  
Salvatore Siciliano ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Sex Ratio ◽  
Population Size ◽  
Effective Population Size ◽  
Tursiops Truncatus ◽  
Bottlenose Dolphins ◽  
Sao Paulo ◽  
Primary Concern ◽  
São Paulo ◽  
Effective Population

The São Pedro and São Paulo Archipelago (SPSPA) (00°56’N, 29°22’W) lies approximately 1010km northeast off the coast of Rio Grande do Norte State in Brazilian waters. Recently, through photo-identification and group size analysis, around 20-30 individual bottlenose dolphins, Tursiops truncatus, from SPSPA were recognized as a resident, and potentially genetically isolated, population. The effective population size (Ne), not the census number (Nc), as well the sex ratio, are of primary concern from an evolutionary and conservation management perspectives. The estimate of Ne reflects the number of individuals responsible for the maintenance of genetic diversity of a species or population as well its evolutionary potential. For this reason, we present here the first Ne and sex ratio estimates for the bottlenose dolphin population from SPSPA. Sex was molecularly determined for 19 biopsy samples collected from bottlenose dolphins from SPSPA between January and February 2005. The Newas estimated by direct counting of reproductive adults sexed by DNA analysis. The resulting Ne was 12 individuals and the sex ratio was 1.11 male to 1 female, however, it was not significantly different from the expected 1:1 ratio (χ2 test, α= 0.05; df = 1). The effective population size based on the genetic diversity of 19 sequences of the mtDNA control region resulted in a female effective population size of 223 individuals, and the total long-term effective size of ~470 individuals. We believe that the estimated Ne for the SPSPA population is a critical value, because it is significantly lower than the mean minimum viable population (MVP) suggested for vertebrates (around 5000 breeding age adults). This small Ne is of great concern and should be taken into account in future management plans to ensure the conservation and protection of this small population at SPSPA.

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