scholarly journals Structure and genetic variability of the Mexican Sardo Negro breed

2022 ◽  
Vol 52 (5) ◽  
Author(s):  
Joel Domínguez-Viveros ◽  
Antonio Reyes-Cerón ◽  
Juan Fernando Saiz-Pineda ◽  
Cesar Villegas-Gutiérrez ◽  
Guadalupe Nelson Aguilar-Palma ◽  
...  
Keyword(s):  
Genetic Variability ◽  
Population Genetic ◽  
Genetic Parameters ◽  
Inbreeding Coefficient ◽  
Structure Evolution ◽  
Effective Number ◽  
Effective Population ◽  
Population Genetic Parameters ◽  
Additive Genetic Relationship ◽  
Over Time

ABSTRACT: This study analyzed the Sardo Negro breed pedigree (41,521 animals registered from 1958 to 2019) to determine its structure, evolution, and genetic variability (GV). The population genetic parameters evaluated were effective number of founders (fe) and ancestors (fa), pedigree integrity, additive genetic relationship (AGR); number of complete generations (NCG), maximum generations traced (NMGT), and equivalent complete generations (NECG); effective population size (Ne), inbreeding coefficient (F), and generation interval (GI). The average GI was 7.45 years. A total of 7,804 founders and 4,856 ancestors were identified for a fe of 185 and a fa of 97. The average and maximum values of NCG, NECG, and NMGT were 1.6 and 5.0, 2.5 and 6.5, 4.3 and 12, with Ne estimates of 15.9, 25.9, and 69.0, respectively. The increase in F, linked to Ne, ranged from 0.72% to 3.1% per generation. The average values for F and AGR were 3.6% and 1.0%, respectively. The proportion of inbred individuals was 32.0%, with F values ranging from 0.01 to 62.2% and an average of 11.3%. The rate of inbred population was 1.3% per year. The annual rate of AGR was 0.04%. For the continuity and projection of the breed, the evolution of F as a function of Ne and the possible implications of the selection schemes must be considered. The genetic variability sustained over time results from the Ne.

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 IDENTITY COEFFICIENTS IN FINITE POPULATIONS. I. EVOLUTION OF IDENTITY COEFFICIENTS IN A RANDOM MATING DIPLOID DIOECIOUS POPULATION

Genetics ◽  
1977 ◽  
Vol 86 (3) ◽  
pp. 697-713
Author(s):  
C Chevalet ◽  
M Gillois ◽  
R F Nassar
Keyword(s):  
Genetic Variability ◽  
Population Size ◽  
Effective Population Size ◽  
Random Mating ◽  
Matrix Multiplication ◽  
Inbred Lines ◽  
Inbreeding Coefficient ◽  
Effective Population ◽  
The Mean ◽  
Over Time

ABSTRACT Properties of identity relation between genes are discussed, and a derivation of recurrent equations of identity coefficients in a random mating, diploid dioecious population is presented. Computations are run by repeated matrix multiplication. Results show that for effective population size (Ne) larger than 16 and no mutation, a given identity coefficient at any time t can be expressed approximately as a function of (1—f), (1—f)3 and (1—f)6, where f is the mean inbreeding coefficient at time t. Tables are presented, for small Ne values and extreme sex ratios, showing the pattern of change in the identity coefficients over time. The pattern of evolution of identity coefficients is also presented and discussed with respect to N eu, where u is the mutation rate. Applications of these results to the evolution of genetic variability within and between inbred lines are discussed.

Pedigree-based analysis of genetic variability in the registered Normande cattle breed in Colombia

2017 ◽  
Vol 57 (3) ◽  
pp. 422
Author(s):  
Derly Rodríguez Sarmiento ◽  
Emanuela Tullo ◽  
Rita Rizzi
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Population Size ◽  
Cattle Breed ◽  
Inbreeding Coefficient ◽  
Mating Strategies ◽  
Effective Population ◽  
Significant Difference ◽  
Genealogical Information ◽  
Over Time

Genetic variability and structure of the population were studied in 7949 registered Normande cattle in Colombia. The pedigree was deep with 18 traced generations, but there were some incomplete genealogical information for the cattle born in the more distant past. The average number of complete and equivalent complete generations was 2.42 and 5.21, respectively. The average pedigree completeness index for five generations was 0.62, which increased over time, and a significant difference between sexes was found (males: 0.82 ± 0.11; females: 0.62 ± 0.38). The average generation interval was 7.57 years. The number of founders, effective founders, ancestors, and founder genomes were 575, 115, 47, and 22.22, respectively, which suggests that an unequal use of founders and a random loss of alleles from founders occurred over time. The level of inbreeding was 0.019 and increased to 0.023, when the inbreeding coefficient was calculated by assigning inbreeding of contemporaries to founders. These levels of inbreeding lead to an effective population size of 138.5 and 117.9 and to a 0.36% and 0.42% rate of inbreeding, respectively. Out of 267 herds with more than five registered breeding animals, only one nucleus herd was present, whereas 117 and 119 were classified as multiplier and commercial herds, respectively. About 92% of calves were sired by French bulls; but the use of Colombian bulls for breeding is increasing. The Colombian Normande breed is at an acceptable level of genetic variability, although some losses of founder alleles have occurred. As the level of inbreeding has been increasing, inbreeding and mating strategies should be monitored in order to maintain the genetic diversity of the breed.

scholarly journals The Limits to Estimating Population-Genetic Parameters with Temporal Data

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.

scholarly journals Genetic analysis of the Hungarian population of endangered Hucul horses

2018 ◽  
Vol 63 (No. 6) ◽  
pp. 237-246 ◽  
Author(s):  
E. Somogyvári ◽  
J. Posta ◽  
S. Mihók
Keyword(s):  
Population Genetic ◽  
Inbreeding Coefficient ◽  
Genome Equivalent ◽  
Effective Number ◽  
Effective Population ◽  
Horse Population ◽  
Inbreeding Coefficients ◽  
Hungarian Population ◽  
Loss Of Genetic Diversity ◽  
Reference Stock

The population genetic evaluation of the Hungarian Hucul horse population was performed based on pedigree records. Herd book data of registered Hucul horses available up to 2016 were analysed using ENDOG (Gutierrez and Goyache 2005) and POPREP (Groeneveld et al. 2009) on the whole population (WP) as well as on the reference stock (RS) (breeding stock registered in 2016). Inbreeding coefficients were 5.57% (WP) and 7.18% (RS). Average relatedness was 10.39% in WP and higher in RS (12.67%). Effective population size was 52.32. Generation interval was 13.01 years for WP and 10.99 years for RS. The values for equivalent complete generations were 6.07 and 8.75, for the maximum number of generations 14.11 and 19.16, and for the number of full generations traced 3.77 and 5.50 for WP and RS, respectively. The effective number of founders (f<sub>e</sub>) was 23 both for WP and RS. The effective number of ancestors (f<sub>a</sub>) was 20 in WP and lower in RS (16). The f<sub>a</sub>/f<sub>e</sub> ratio was 0.869 in WP and 0.696 in RS. Founder genome equivalent (f<sub>g</sub>) was 9.618 in WP and 5.790 in RS. The f<sub>g</sub>/f<sub>e</sub> ratio was 0.481 in WP and 0.361 in RS. The study revealed that both the inbreeding coefficient and the average relatedness were high. The above mentioned ratios indicated loss of genetic diversity in the Hungarian Hucul population.

Estimation of population genetic parameters using an EM algorithm and sequence data from experimental evolution populations

2019 ◽  
Vol 36 (1) ◽  
pp. 221-231 ◽  
Author(s):  
Yasuhiro Kojima ◽  
Hirotaka Matsumoto ◽  
Hisanori Kiryu
Keyword(s):  
Allele Frequency ◽  
Population Genetic ◽  
Genetic Parameters ◽  
Sequence Data ◽  
Expectation Maximization Algorithm ◽  
Supplementary Information ◽  
Effective Population ◽  
Forward Equation ◽  
Population Genetic Parameters ◽  
Frequency Changes

Abstract Motivation Evolve and resequence (E&R) experiments show promise in capturing real-time evolution at genome-wide scales, enabling the assessment of allele frequency changes SNPs in evolving populations and thus the estimation of population genetic parameters in the Wright–Fisher model (WF) that quantify the selection on SNPs. Currently, these analyses face two key difficulties: the numerous SNPs in E&R data and the frequent unreliability of estimates. Hence, a methodology for efficiently estimating WF parameters is needed to understand the evolutionary processes that shape genomes. Results We developed a novel method for estimating WF parameters (EMWER), by applying an expectation maximization algorithm to the Kolmogorov forward equation associated with the WF model diffusion approximation. EMWER was used to infer the effective population size, selection coefficients and dominance parameters from E&R data. Of the methods examined, EMWER was the most efficient method for selection strength estimation in multi-core computing environments, estimating both selection and dominance with accurate confidence intervals. We applied EMWER to E&R data from experimental Drosophila populations adapting to thermally fluctuating environments and found a common selection affecting allele frequency of many SNPs within the cosmopolitan In(3R)P inversion. Furthermore, this application indicated that many of beneficial alleles in this experiment are dominant. Availability and implementation Our C++ implementation of ‘EMWER’ is available at https://github.com/kojikoji/EMWER. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Ecological correlates of population genetic structure: a comparative approach using a vertebrate metacommunity

2006 ◽  
Vol 273 (1604) ◽  
pp. 3001-3009 ◽  
Author(s):  
Mollie K Manier ◽  
Stevan J Arnold
Keyword(s):  
Species Interactions ◽  
Population Genetic ◽  
Genetic Parameters ◽  
Species Abundance ◽  
Comparative Approach ◽  
Effective Population ◽  
Ecological Data ◽  
Population Genetic Differentiation ◽  
Ecological Correlates ◽  
Population Genetic Parameters

Identifying ecological factors associated with population genetic differentiation is important for understanding microevolutionary processes and guiding the management of threatened populations. We identified ecological correlates of several population genetic parameters for three interacting species (two garter snakes and an anuran) that occupy a common landscape. Using multiple regression analysis, we found that species interactions were more important in explaining variation in population genetic parameters than habitat and nearest-neighbour characteristics. Effective population size was best explained by census size, while migration was associated with differences in species abundance. In contrast, genetic distance was poorly explained by the ecological correlates that we tested, but geographical distance was prominent in models for all species. We found substantially different population dynamics for the prey species relative to the two predators, characterized by larger effective sizes, lower gene flow and a state of migration-drift equilibrium. We also identified an escarpment formed by a series of block faults that serves as a barrier to dispersal for the predators. Our results suggest that successful landscape-level management should incorporate genetic and ecological data for all relevant species, because even closely associated species can exhibit very different population genetic dynamics on the same landscape.

scholarly journals Population genetic characteristics of horse chestnut in Serbia

2013 ◽  
Vol 65 (1) ◽  
pp. 1-7 ◽  
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.

scholarly journals Population structure of Czech cold-blooded breeds of horses

2011 ◽  
Vol 54 (1) ◽  
pp. 1-9
Author(s):  
L. Vostrý ◽  
Z. Čapková ◽  
J. Přibyl ◽  
B. Hofmanová ◽  
H. Vostrá Vydrová ◽  
...  
Keyword(s):  
Population Structure ◽  
Genetic Variability ◽  
Population Size ◽  
Effective Population Size ◽  
Inbreeding Coefficient ◽  
Effective Population ◽  
The Czech Republic ◽  
Generation Interval ◽  
Average Value ◽  
Inbreeding Coefficients

Abstract. In order to estimate effective population size, generation interval and the development of inbreeding coefficients (Fx) in three original breeds of cold-blooded horses kept in the Czech Republic: Silesian Noriker (SN), Noriker (N) and Czech-Moravian Belgian horse (CMB) all animals of the particular breeds born from 1990 to 2007 were analysed. The average values of generation interval between parents and their offspring were: 8.53 in SN, 8.88 in N and 8.56 in CMB. Average values of effective population size were estimated to be: 86.3 in SN, 162.3 in N and 104.4 in CMB. The average values of inbreeding coefficient were 3.13 % in SN stallions and 3.39 % in SN mares, in the N breed 1.76 % and 1.26 % and in the CMB breed 3.84 % and 3.26 % respectively. Overall averages of Fx were: 3.23 %, 1.51 % and 3.55 % for the breeds SN, N and CMB. The average value of inbreeding coefficient Fx increased by 1.22 % in SN, by 0.35 % in N and by 1.01 % in CMB, respectively. This may lead to a reduction in genetic variability. Reduction in genetic variability could be either controlled in cooperation with corresponding populations of cold-blooded breeds in other European countries or controlled by number of sires used in population

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