On the number of reproductives contributing to a half-sib progeny array

We address various statistical aspects of biological parentage in multi-offspring broods that arise via multiple paternity or multiple maternity and, hence, consist of mixtures of full- and half-sibs. Conditioned on population genetic parameters, computer simulations described herein permit estimation of: (1) the mean number of offspring needed to detect all parental gametes in a brood and (2) the relationship between the number of distinct parental gametes found in a brood and the number of parents. Results are relevant to the design of empirical studies employing molecular markers to assess genetic parentage in polygynous or polyandrous species with large broods, such as are found in many fishes, amphibians, insects, plants and other groups. The utility of this approach is illustrated using two empirical data sets.

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Distributional characterizations and testing for differences of relatedness and inbreeding of a subpopulation of American Hereford bulls

Translational Animal Science ◽

10.1093/tas/txab008 ◽

2021 ◽

Vol 5 (1) ◽

Author(s):

M A Simmons ◽

P K Riggs ◽

S Sanders ◽

A D Herring ◽

J O Sanders ◽

...

Keyword(s):

Beta Distribution ◽

Genetic Parameters ◽

Inbreeding Coefficient ◽

Bootstrap Sampling ◽

Inbreeding Coefficients ◽

Beta Distributions ◽

Relationship Coefficient ◽

The Mean ◽

Population Genetic Parameters ◽

The Relationship

Abstract Beta distributions are characterized by two determining parameters and a parameter space from 0 to 1, and may be useful for examining population genetic parameters such as the relationship or inbreeding coefficients. Often subpopulations exist within breeds that are congregated around particular lineages of cattle or ancestors that breeders value. These subpopulations are more related to each other than to the majority of other animals; they may have higher inbreeding as well. Value may be added to these subpopulations because of their relatedness with important or renowned ancestors. The objectives of this work were to compare the relatedness and inbreeding of a group of 26 modern bulls from a subpopulation of the American Hereford breed relative to 1) 30 males with the most descendants present in the pedigree, 2) 15 renowned American Hereford bulls considered important individuals in the breed’s history, and 3) 19 prominent subpopulation male ancestors. Conformance of the mean relationship coefficients of the bulls with the three groups and the mean inbreeding coefficient with all pedigree animals to beta distributions was assessed by 1) visually determining the parameters of the beta distributions based on the entire pedigree, 2) testing the mean relationship coefficient or inbreeding coefficient of the group of subpopulation bulls for its positional inclusion in those distributions, and 3) bootstrap sampling methodology. The mean relationship coefficients of the 26 Trask bulls with the 30 bulls with the most descendants, the 15 renowned ancestors, and the 19 Trask male ancestors were 0.15, 0.132, and 0.208, respectively. Testing of these means in beta distributions indicated that the group of 26 Trask bulls were no more related to the three groups of bulls than all of the animals in the pedigree (0.06 < P < 0.25). Bootstrap sampling indicated that the 26 bulls were more related to the three groups of male ancestors than the remainder of the animals in the pedigree (P < 0.0001). The mean inbreeding coefficient of the 26 bulls (0.13) did not differ from the overall inbreeding coefficient (0.056) when tested using a beta distribution; however, bootstrap sampling indicated otherwise (P < 0.0001). Results may indicate the inadequacy of visually parameterizing a beta distribution. Quantification of pedigree relatedness of a group of animals to key ancestors, especially with no DNA available, may add value to that group and individuals.

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Population genetic characteristics of horse chestnut in Serbia

Archives of Biological Sciences ◽

10.2298/abs1301001o ◽

2013 ◽

Vol 65 (1) ◽

pp. 1-7 ◽

Cited By ~ 2

Author(s):

Mirjana Ocokoljic ◽

Dragica Vilotic ◽

Mirjana Sijacic-Nikolic

Keyword(s):

Population Genetic ◽

Genetic Parameters ◽

Individual Variability ◽

Horse Chestnut ◽

Statistical Parameters ◽

Genetic Characteristics ◽

Different Populations ◽

Growth Phenotype ◽

Population Genetic Parameters ◽

Cultivated Populations

The general population genetic characteristics of cultivated horse chestnut trees excelling in growth, phenotype characteristics, type of inflorescence, productivity and resistance to the leafminer Cameraria ohridella Deschka and Dimic were analyzed in Serbia. The analyzed population genetic parameters point to fundamental differences in the genetic structure among the cultivated populations in Serbia. The study shows the variability in all properties among the populations and inter-individual variability within the populations. The variability and differential characteristics were assessed using statistical parameters, taking into account the satisfactory reflection of the hereditary potential. The assessed differences in the vitality and evolution potential of different populations can determine the methods of horse chestnut gene pool collection, reconstruction and improvement.

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Inferring Population Genetic Parameters: Particle Filtering, HMM, Ripley’s K-Function or Runs of Homozygosity?

Lecture Notes in Computer Science - Algorithms in Bioinformatics ◽

10.1007/978-3-319-43681-4_19 ◽

2016 ◽

pp. 234-245

Author(s):

Svend V. Nielsen ◽

Simon Simonsen ◽

Asger Hobolth

Keyword(s):

Particle Filtering ◽

Population Genetic ◽

Genetic Parameters ◽

Runs Of Homozygosity ◽

Ripley’S K Function ◽

Ripley’S K ◽

Ripley's K ◽

Population Genetic Parameters ◽

K Function

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Selection criteria for scoring amplified fragment length polymorphisms (AFLPs) positively affect the reliability of population genetic parameter estimates

Genome ◽

10.1139/g10-006 ◽

2010 ◽

Vol 53 (4) ◽

pp. 302-310 ◽

Cited By ~ 32

Author(s):

Doris Herrmann ◽

Bénédicte N. Poncet ◽

Stéphanie Manel ◽

Delphine Rioux ◽

Ludovic Gielly ◽

...

Keyword(s):

Genetic Diversity ◽

Fragment Length ◽

Population Genetic ◽

Selection Criteria ◽

Genetic Parameters ◽

Data Set ◽

Marker Selection ◽

Length Polymorphisms ◽

Amplified Fragment Length Polymorphisms ◽

Population Genetic Parameters

A reliable data set is a fundamental prerequisite for consistent results and conclusions in population genetic studies. However, marker scoring of genetic fingerprints such as amplified fragment length polymorphisms (AFLPs) is a highly subjective procedure, inducing inconsistencies owing to personal or laboratory-specific criteria. We applied two alternative marker selection algorithms, the newly developed script scanAFLP and the recently published AFLPScore, to a large AFLP genome scan to test how population genetic parameters and error rates were affected. These results were confronted with replicated random selections of marker subsets. We show that the newly developed marker selection criteria reduced the mismatch error rate and had a notable influence on estimates of genetic diversity and differentiation. Both effects are likely to influence biological inference. For example, genetic diversity (HS) was 29% lower while genetic differentiation (FST) was 8% higher when applying scanAFLP compared with AFLPScore. Likewise, random selections of markers resulted in substantial deviations of population genetic parameters compared with the data sets including specific selection criteria. These randomly selected marker sets showed surprisingly low variance among replicates. We conclude that stringent marker selection and phenotype calling reduces noise in the data set while retaining patterns of population genetic structure.

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Use of RAPD analyses to estimate population genetic parameters in the alfalfa leaf-cutting bee, Megachile rotundata

Genome ◽

10.1139/g96-083 ◽

1996 ◽

Vol 39 (4) ◽

pp. 655-663 ◽

Cited By ~ 13

Author(s):

Rui Lu ◽

Gerald H. Rank

Keyword(s):

Genetic Distance ◽

Population Genetic ◽

Rapd Markers ◽

Genetic Parameters ◽

Megachile Rotundata ◽

Isolated Populations ◽

Leaf Cutting ◽

Nucleotide Divergence ◽

Alfalfa Leaf ◽

Population Genetic Parameters

RAPD analyses were performed on five geographically isolated populations of Megachile rotundata. We used haploid males of the alfalfa leaf-cutting bee, M. rotundata, to overcome the limitation of the dominance of RAPD markers in the determination of population genetic parameters. Sixteen primers gave rise to 130 polymorphic and 31 monomorphic bands. The unbiased estimators calculated in this study include within- and between-population heterozygosity, nucleotide divergence, and genetic distance. The genetic diversity (H = 0.32–0.35) was found to be about 10 times that of previous estimates (H = 0.033) based on allozyme data. Contrary to the data obtained at the protein level, our results suggest that Hymenoptera do not have a lower level of genetic variability at the DNA level compared with other insect species. Regardless of the different assumptions underlying the calculation of heterozygosity, divergence, and genetic distance, all five populations showed a parallel interrelationship for the three parameters. We conclude that RAPD markers are a convenient tool to estimate population genetic variation in haploid M. rotundata and that with an adequate sample size the technique is applicable to the evaluation of divergence in diploid populations. Key words : Megachile rotundata, RAPD, heterozygosity, genetic distance, nucleotide divergence.

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A preliminary analysis of the population genetic parameters indicates critically low genetic variation in a threatened killifish ( Anatolichthys transgrediens )

Journal of Applied Ichthyology ◽

10.1111/jai.14289 ◽

2021 ◽

Author(s):

Baran Yoğurtçuoğlu ◽

Murat Yılmaz ◽

Fitnat Güler Ekmekçi ◽

Ergi Deniz Özsoy

Keyword(s):

Genetic Variation ◽

Preliminary Analysis ◽

Population Genetic ◽

Genetic Parameters ◽

Population Genetic Parameters

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

Amphibia-Reptilia ◽

10.1163/15685381-00003123 ◽

2017 ◽

Vol 38 (4) ◽

pp. 411-424 ◽

Cited By ~ 2

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.

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The Limits to Estimating Population-Genetic Parameters with Temporal Data

Genome Biology and Evolution ◽

10.1093/gbe/evaa056 ◽

2020 ◽

Vol 12 (4) ◽

pp. 443-455

Author(s):

Michael Lynch ◽

Wei-Chin Ho

Keyword(s):

Population Genetic ◽

Genetic Parameters ◽

Natural Populations ◽

Estimation Methods ◽

Frequency Change ◽

Sampling Variance ◽

Effective Population ◽

Closed Population ◽

Temporal Variance ◽

Population Genetic Parameters

Abstract The ability to obtain genome-wide sequences of very large numbers of individuals from natural populations raises questions about optimal sampling designs and the limits to extracting information on key population-genetic parameters from temporal-survey data. Methods are introduced for evaluating whether observed temporal fluctuations in allele frequencies are consistent with the hypothesis of random genetic drift, and expressions for the expected sampling variances for the relevant statistics are given in terms of sample sizes and numbers. Estimation methods and aspects of statistical reliability are also presented for the mean and temporal variance of selection coefficients. For nucleotide sites that pass the test of neutrality, the current effective population size can be estimated by a method of moments, and expressions for its sampling variance provide insight into the degree to which such methodology can yield meaningful results under alternative sampling schemes. Finally, some caveats are raised regarding the use of the temporal covariance of allele-frequency change to infer selection. Taken together, these results provide a statistical view of the limits to population-genetic inference in even the simplest case of a closed population.

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