scholarly journals Palliating the impact of fixation of a major gene on the genetic variation of artificially selected polygenes

2006 ◽  
Vol 88 (2) ◽  
pp. 105-118 ◽  
Author(s):  
LEOPOLDO SÁNCHEZ ◽  
ARMANDO CABALLERO ◽  
ENRIQUE SANTIAGO
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Selective Sweep ◽  
Major Gene ◽  
Optimal Path ◽  
Fixation Time ◽  
Selection Intensity ◽  
Effective Population ◽  
The Impact ◽  
Polygenic Variation

Selective sweeps of variation caused by fixation of major genes may have a dramatic impact on the genetic gain from background polygenic variation, particularly in the genome regions closely linked to the major gene. The response to selection can be restrained because of the reduced selection intensity and the reduced effective population size caused by the increase in frequency of the major gene. In the context of a selected population where fixation of a known major gene is desired, the question arises as to which is the optimal path of increase in frequency of the gene so that the selective sweep of variation resulting from its fixation is minimized. Using basic theoretical arguments we propose a frequency path that maximizes simultaneously the effective population size applicable to the selected background and the selection intensity on the polygenic variation by minimizing the average squared selection intensity on the major gene over generations up to a given fixation time. We also propose the use of mating between carriers and non-carriers of the major gene, in order to promote the effective recombination between the major gene and its linked polygenic background. Using a locus-based computer simulation assuming different degrees of linkage, we show that the path proposed is more effective than a similar path recently published, and that the combination of the selection and mating methods provides an efficient way to palliate the negative effects of a selective sweep.

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.

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 Impact of fertility variation on genetic diversity and phenotypic traits in second generation seed production areas and clonal seed orchards of Eucalyptus camaldulensis

2019 ◽  
Vol 68 (1) ◽  
pp. 29-40
Author(s):  
P.G. Suraj ◽  
K. Nagabhushana ◽  
R. Kamalakannan ◽  
M. Varghese
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Effective Population Size ◽  
Second Generation ◽  
Gene Diversity ◽  
Eucalyptus Camaldulensis ◽  
Phenotypic Traits ◽  
Effective Population ◽  
Fertility Variation ◽  
The Impact

Abstract Fertility and gene diversity were estimated in three second generation (F2) seed stands (SPA 1-3) and two clone trials (CSO 1&2) of Eucalyptus camaldulensis to assess the impact on seed crop. F2 seedlots were evaluated in comparison to native provenances, ten commercial clones and interspecific hybrids at diverse sites. SPA 1&2 were genetic gain trials of five first generation (F1) orchard seedlots, SPA 3 a plantation of one F1 orchard seedlot, and CSOs were clone trials of 21 commercial clones established at two contrasting sites. Fertility variation, as indicated by sibling coefficient, was high (Ψ, 9-14) in the SPAs as only about 26 % trees were fertile compared to 81 % trees in CSOs. Effective population size was higher in SPA 1 and 2 (Ns, 95 and 74, respectively) than SPA 3 (Ns = 39). Fertility was highly skewed in CSO 2 resulting in low effective population size (Ns = 2) compared to CSO 1 (Ns = 11). Constant seed collection enabled 3-fold increase in relative population size and 22 % higher predicted gene diversity in CSO 2. Genetic diversity (He) estimated using SSR markers was higher in SPA 1&2 and native provenances (NAT), compared to SPA 3 and CSO 1, whereas CSO 2 and clones had lower values. There was a high positive correlation between estimated He and predicted gene diversity values of SPAs and CSOs. He was positively correlated to mean field survival and negatively correlated to kraft pulp yield (KPY), evaluated at three years in progeny trials across three locations. Number of alleles per locus was higher in SPAs and native provenances compared to CSOs and clones. Discriminant principal component analysis clustered CSO, NAT and SPA seedlots in different groups while commercial E. camaldulensis clones clustered close to NAT. Multilocus outcrossing rate was generally high (tm, 91-100 %), though selfing was observed in two families of SPA 3 and CSO 2. Selected interspecific hybrid families of commercial E. camaldulensis clones (with E. urophylla and E. pellita) evaluated at two of the sites had higher He and KPY than clones at three years.

scholarly journals EFFECTS OF POPULATION SIZE AND SELECTION INTENSITY ON CORRELATED RESPONSES TO SELECTION FOR POSTWEANING GAIN IN MICE

Genetics ◽  
1973 ◽  
Vol 74 (1) ◽  
pp. 157-170
Author(s):  
E J Eisen ◽  
J P Hanrahan ◽  
J E Legates
Keyword(s):  
Body Weight ◽  
Population Size ◽  
Effective Population Size ◽  
Litter Size ◽  
The Body ◽  
Selection Intensity ◽  
Correlated Responses ◽  
Effective Population ◽  
Population Sizes ◽  
Selection For

ABSTRACT Correlated responses to selection for postweaning gain in mice were studied to determine the influence of population size and selection intensity. Correlated traits measured were three-, six- and eight-week body weights, litter size, twelve-day litter weight, proportion infertile matings and two indexes of reproductive performance. In general, the results agreed with observations made on direct response: correlated responses in the body weight traits and litter size increased as (1) selection intensity increased and (2) effective population size increased. Correlated responses in the body weight traits and litter size were positive in the large population size lines (16 pairs), as expected from the positive genetic correlation between these traits and postweaning gain. However, several negative correlated responses were observed at small population sizes (one and two pairs). Within each level of selection intensity, traits generally associated with fitness tended to decline most in the very small populations (one and two pairs) and in the large populations (16 pairs) for apparently different reasons. The fitness decline at the small effective population sizes was attributable to inbreeding depression. In contrast, it was postulated that the fitness decline at the large effective population size was due to selection moving the population mean for body weight and a trait positively correlated genetically with body weight (i.e., percent body fat) away from an optimum

scholarly journals Historical effective population size of North American hoary bat (Lasiurus cinereus) and challenges to estimating trends in contemporary effective breeding population size from archived samples

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11285
Author(s):  
Robert S. Cornman ◽  
Jennifer A. Fike ◽  
Sara J. Oyler-McCance ◽  
Paul M. Cryan
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
North American ◽  
Breeding Population ◽  
Data Filtering ◽  
Effective Population ◽  
Data Set ◽  
Lasiurus Cinereus ◽  
The Impact ◽  
Hoary Bats

Background Hoary bats (Lasiurus cinereus) are among the bat species most commonly killed by wind turbine strikes in the midwestern United States. The impact of this mortality on species census size is not understood, due in part to the difficulty of estimating population size for this highly migratory and elusive species. Genetic effective population size (Ne) could provide an index of changing census population size if other factors affecting Ne are stable. Methods We used the NeEstimator package to derive effective breeding population size (Nb) estimates for two temporally spaced cohorts: 93 hoary bats collected in 2009–2010 and an additional 93 collected in 2017–2018. We sequenced restriction-site associated polymorphisms and generated a de novo genome assembly to guide the removal of sex-linked and multi-copy loci, as well as identify physically linked markers. Results Analysis of the reference genome with psmc suggested at least a doubling of Ne in the last 100,000 years, likely exceeding Ne = 10,000 in the Holocene. Allele and genotype frequency analyses confirmed that the two cohorts were comparable, although some samples had unusually high or low observed heterozygosities. Additionally, the older cohort had lower mean coverage and greater variability in coverage, and batch effects of sampling locality were observed that were consistent with sample degradation. We therefore excluded samples with low coverage or outlier heterozygosity, as well as loci with sequence coverage far from the mode value, from the final data set. Prior to excluding these outliers, contemporary Nb estimates were significantly higher in the more recent cohort, but this finding was driven by high values for the 2018 sample year and low values for all other years. In the reduced data set, Nb did not differ significantly between cohorts. We found base substitutions to be strongly biased toward cytosine to thymine or the complement, and further partitioning loci by substitution type had a strong effect on Nb estimates. Minor allele frequency and base quality bias thresholds also had strong effects on Nb estimates. Instability of Nb with respect to common data filtering parameters and empirically identified factors prevented robust comparison of the two cohorts. Given that confidence intervals frequently included infinity as the stringency of data filtering increased, contemporary trends in Nb of North American hoary bats may not be tractable with the linkage disequilibrium method, at least using the protocol employed here.

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 Genetic Diversity and the Impact of the Breed Proportions of US Brown Swiss in German Brown Cattle

Animals ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 152
Author(s):  
Anna Wirth ◽  
Jürgen Duda ◽  
Ottmar Distl
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Effective Population Size ◽  
Reference Population ◽  
Pedigree Data ◽  
Effective Population ◽  
Brown Swiss ◽  
Inbreeding Coefficients ◽  
Loss Of Genetic Diversity ◽  
The Impact

Increase of inbreeding and loss of genetic diversity have large impact on farm animal genetic resources. Therefore, the aims of the present study were to analyse measures of genetic diversity as well as recent and ancestral inbreeding using pedigree data of the German Brown population, and to identify causes for loss of genetic diversity. The reference population included 922,333 German Brown animals born from 1990 to 2014. Pedigree depth and completeness reached an average number of complete equivalent generations of 6.24. Estimated effective population size for the German Brown reference population was about 112 with a declining trend from 141 to 95 for the birth years. Individual inbreeding coefficients increased from 0.013 to 0.036. Effective number of founders, ancestors and founder genomes of 63.6, 36.23 and 20.34 indicated unequal contributions to the reference population. Thirteen ancestors explained 50% of the genetic diversity. Higher breed proportions of US Brown Swiss were associated with higher levels of individual inbreeding. Ancestral inbreeding coefficients, which are indicative for exposure of ancestors to identical-by-descent alleles, increased with birth years but recent individual inbreeding was higher than ancestral inbreeding. Given the increase of inbreeding and decline of effective population size, measures to decrease rate of inbreeding and increase effective population size through employment of a larger number of sires are advisable.

scholarly journals Effects of Artificial Selection on Rates of Inbreeding in Populations of Drosophila Melanogaster

1969 ◽  
Vol 22 (1) ◽  
pp. 157 ◽  
Author(s):  
LP Jones
Keyword(s):  
Drosophila Melanogaster ◽  
Genetic Variation ◽  
Population Size ◽  
Effective Population Size ◽  
Artificial Selection ◽  
Selection Intensity ◽  
Base Population ◽  
Next Generation ◽  
Effective Population ◽  
Bristle Number

Three lines from the Canberra base population were selected for increased abdominal bristle number for up to 28 generations with 10 pairs of parents and 20% selection intensity. The effective population size as measured by either variance of family contributions to the next generation or by the rate of inbreeding was gener-ally lowest when the lines were responding rapidly to selection. Consideration of the contributions of families in any generation to the lines five generations later showed that much of the genetic variation came from only few families in some generations.

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