Effective population size and genetic structure of a Piute ground squirrel (Spermophilus mollis) population

2001 ◽  
Vol 79 (1) ◽  
pp. 26-34 ◽  
Author(s):  
Michael F Antolin ◽  
Beatrice Van Horne ◽  
Michael D Berger, Jr. ◽  
Alisha K Holloway ◽  
Jennifer L Roach ◽  
...  
Keyword(s):  
Genetic Analysis ◽  
Population Size ◽  
Effective Population Size ◽  
Ground Squirrel ◽  
Population Genetic ◽  
Ground Squirrels ◽  
Perennial Grasses ◽  
Population Subdivision ◽  
Effective Population ◽  
Population Genetic Analysis

Piute ground squirrels (Spermophilus mollis) are distributed continuously in habitat dominated by native shrubs and perennial grasses in the Snake River Birds of Prey National Conservation Area in Idaho, U.S.A. This habitat is being fragmented and replaced by exotic annual plants, changing it to a wildfire-dominated system that provides poor habitat for ground squirrels. To assess potential effects of this fragmentation on ground squirrel populations, we combined an estimate of effective population size (Ne) based upon a demographic study with a population genetic analysis. The study area included three subpopulations separated from each other by 8–13 km. The ratio of effective population size to census number (Ne/N) was 0.57. Combining Ne/N with dispersal distances from a radio-tracking study, we calculated that neighborhood size was 62.2 ha, which included between 204 and 480 individuals. Our population genetic analysis (based on randomly amplified polymorphic DNA (RAPD) and microsatellite markers) showed relatively low levels of genetic differentiation (Qpopulations [Formula: see text] 0.07–0.10) between subpopulations and no inbreeding within subpopulations (f = 0.0003). These estimates of population subdivision translate into an effective migration rate (Nem) of 2.3–3.3 per year, which represents a high level of gene flow. Invasion by exotics will reduce the overall productivity of the habitat, and will lead to isolation among subpopulations if favorable habitat patches become isolated.

scholarly journals A phylogenetic estimator of effective population size or mutation rate.

Genetics ◽  
1994 ◽  
Vol 136 (2) ◽  
pp. 685-692 ◽  
Author(s):  
Y X Fu
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Mutation Rate ◽  
Dna Sequences ◽  
High Efficiency ◽  
Minimum Variance ◽  
Population Subdivision ◽  
Effective Population ◽  
Fisher Model ◽  
Mitochondrial Sequences

Abstract A new estimator of the essential parameter theta = 4Ne mu from DNA polymorphism data is developed under the neutral Wright-Fisher model without recombination and population subdivision, where Ne is the effective population size and mu is the mutation rate per locus per generation. The new estimator has a variance only slightly larger than the minimum variance of all possible unbiased estimators of the parameter and is substantially smaller than that of any existing estimator. The high efficiency of the new estimator is achieved by making full use of phylogenetic information in a sample of DNA sequences from a population. An example of estimating theta by the new method is presented using the mitochondrial sequences from an American Indian population.

Effective population size and genetic structure of a Piute ground squirrel (Spermophilus mollis) population

2001 ◽  
Vol 79 (1) ◽  
pp. 26-34 ◽  
Author(s):  
Michael F. Antolin ◽  
Beatrice Van Horne ◽  
Michael D. Berger, Jr. ◽  
Alisha K. Holloway ◽  
Jennifer L. Roach ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Population Size ◽  
Effective Population Size ◽  
Ground Squirrel ◽  
Effective Population

scholarly journals Genetic Diversity, Structure and Effective Population Size of Old-Growth vs. Second-Growth Populations of Keystone and Long-Lived Conifer, Eastern White Pine (Pinus strobus): Conservation Value and Climate Adaptation Potential

2021 ◽  
Vol 12 ◽  
Author(s):  
Om P. Rajora ◽  
John W. R. Zinck
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Effective Population Size ◽  
Population Genetic ◽  
Conservation Value ◽  
Adaptive Potential ◽  
Effective Population ◽  
White Pine ◽  
Old Growth ◽  
Second Growth

Whether old-growth (OG) forests have higher genetic diversity and effective population size, consequently higher conservation value and climate adaptive potential than second-growth (SG) forests, remain an unresolved issue. We have tested the hypothesis that old-growth forest tree populations have higher genetic diversity, effective population size (NE), climate adaptive potential and conservation value and lower genetic differentiation than second-growth forest tree populations, employing a keystone and long-lived conifer, eastern white pine (EWP; Pinus strobus). Genetic diversity and population structure of old-growth and second-growth populations of eastern white pine (EWP) were examined using microsatellites of the nuclear and chloroplast genomes and single nucleotide polymorphisms (SNPs) in candidate nuclear genes putatively involved in adaptive responses to climate and underlying multilocus genetic architecture of local adaptation to climate in EWP. Old-growth and second-growth EWP populations had statistically similar genetic diversity, inbreeding coefficient and inter-population genetic differentiation based on nuclear microsatellites (nSSRs) and SNPs. However, old-growth populations had significantly higher chloroplast microsatellites (cpSSRs) haploid diversity than second-growth populations. Old-growth EWP populations had significantly higher coalescence-based historical long-term NE than second-growth EWP populations, but the linkage disequilibrium (LD)-based contemporary NE estimates were statistically similar between the old-growth and second-growth EWP populations. Analyses of population genetic structure and inter-population genetic relationships revealed some genetic constitution differences between the old-growth and second-growth EWP populations. Overall, our results suggest that old-growth and second-growth EWP populations have similar genetic resource conservation value. Because old-growth and second-growth EWP populations have similar levels of genetic diversity in genes putatively involved in adaptive responses to climate, old-growth, and second-growth populations may have similar adaptive potential under climate change. Our results could potentially be generalized across most of the boreal and temperate conifer forest trees. Our study contributes to address a long-standing issue, advances research field and knowledge about conservation and ecological and climate adaptation of forest trees.

The Genetic Effective Size of a Population

2018 ◽  
Author(s):  
Bruce Walsh ◽  
Michael Lynch
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Genome Structure ◽  
Population Subdivision ◽  
Effective Population ◽  
Entire Genome ◽  
History Of ◽  
A Site ◽  
The Hill ◽  
New Mutations

The effects of genetic drift usually assume an idealized population of constant size. This chapter shows how the population size for such an idealized population can be replaced with an effective population size for populations with age structure, unequal sex ratios, a history of expansion or contraction, inbreeding, and population subdivision. These demographic features impact the entire genome more or less equally. A relatively recent understanding is that selection at a site can dramatically reduce the local effective population size experienced by nearby linked sites (the Hill-Robertson effect). This can arise from background selection to remove deleterious new mutations or from selective sweeps wherein favorable new mutations are driven toward fixation. The Hill-Robertson effect is a general way to describe the fact that selection at a site makes selection are other linked sites less efficient, and, therefore, more neutral. This chapter discusses the implications of this finding for genome structure.

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 Patterns of Inbreeding Depression and Architecture of the Load in Subdivided Populations

Genetics ◽  
2003 ◽  
Vol 165 (4) ◽  
pp. 2193-2212 ◽  
Author(s):  
Sylvain Glémin ◽  
Joëlle Ronfort ◽  
Thomas Bataillon
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Inbreeding Depression ◽  
Local Population ◽  
Population Subdivision ◽  
Deleterious Mutations ◽  
Effective Population ◽  
Subdivided Populations ◽  
And Migration ◽  
Insight Into

AbstractInbreeding depression is a general phenomenon that is due mainly to recessive deleterious mutations, the so-called mutation load. It has been much studied theoretically. However, until very recently, population structure has not been taken into account, even though it can be an important factor in the evolution of populations. Population subdivision modifies the dynamics of deleterious mutations because the outcome of selection depends on processes both within populations (selection and drift) and between populations (migration). Here, we present a general model that permits us to gain insight into patterns of inbreeding depression, heterosis, and the load in subdivided populations. We show that they can be interpreted with reference to single-population theory, using an appropriate local effective population size that integrates the effects of drift, selection, and migration. We term this the “effective population size of selection” (NeS). For the infinite island model, for example, it is equal to NeS=N(1+m∕hs), where N is the local population size, m the migration rate, and h and s the dominance and selection coefficients of deleterious mutation. Our results have implications for the estimation and interpretation of inbreeding depression in subdivided populations, especially regarding conservation issues. We also discuss the possible effects of migration and subdivision on the evolution of mating systems.

scholarly journals Effective Population Size and Population Subdivision in Demographically Structured Populations

Genetics ◽  
2002 ◽  
Vol 162 (1) ◽  
pp. 501-519 ◽  
Author(s):  
Valérie Laporte ◽  
Brian Charlesworth
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Nuclear Gene ◽  
Structured Populations ◽  
Population Subdivision ◽  
Time Interval ◽  
Effective Population ◽  
Left Eigenvector ◽  
Offspring Number ◽  
The Matrix

AbstractA fast-timescale approximation is applied to the coalescent process in a single population, which is demographically structured by sex and/or age. This provides a general expression for the probability that a pair of alleles sampled from the population coalesce in the previous time interval. The effective population size is defined as the reciprocal of twice the product of generation time and the coalescence probability. Biologically explicit formulas for effective population size with discrete generations and separate sexes are derived for a variety of different modes of inheritance. The method is also applied to a nuclear gene in a population of partially self-fertilizing hermaphrodites. The effects of population subdivision on a demographically structured population are analyzed, using a matrix of net rates of movement of genes between different local populations. This involves weighting the migration probabilities of individuals of a given age/sex class by the contribution of this class to the leading left eigenvector of the matrix describing the movements of genes between age/sex classes. The effects of sex-specific migration and nonrandom distributions of offspring number on levels of genetic variability and among-population differentiation are described for different modes of inheritance in an island model. Data on DNA sequence variability in human and plant populations are discussed in the light of the results.

scholarly journals Sex change and effective population size: implications for population genetic studies in marine fish

Heredity ◽  
2016 ◽  
Vol 117 (4) ◽  
pp. 251-258 ◽  
Author(s):  
I Coscia ◽  
J Chopelet ◽  
R S Waples ◽  
B Q Mann ◽  
S Mariani
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Marine Fish ◽  
Population Genetic ◽  
Sex Change ◽  
Effective Population ◽  
Genetic Studies
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