Information-entropy approach to the analysis of genetic diversity of populations (analytical review)

Kuznetsov, V. M.

doi:10.30766/2072-9081.2022.23.2.159-173

Cited by 4 publications

(3 citation statements)

References 28 publications

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“…Для измерения αи β-разнообразия был предложен ряд статистик: Райта, Нея, Вейра и Кокерхэма, Джоста, Чао, Шеннона/Шервина [10,11,12,13,14,15], которые базируются на разных биологических и математических допущениях. Проводится сравнительный анализ этих мер разнообразия [16,17,18]. Все они способствуют получению той или иной информации о различных аспектах аллельного разнообразия, демографической истории и/или диф-ференциации пород, о структуре генетической изменчивости популяций.…”

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“…Материал и методы. В работе использовали те же данные, что и в предыдущих публикациях [16,17,18]. В частности, 84 быка, каждый генотипирован по 11 STR-локусам (микросателлиты ДНК) 1 : 10 быков джерсейской породы, 10 -айрширской породы, 10 -красной датской, 9 -красной шведской и 45 быков голштинской породы трёх «экотипов» (отродий): 13 быков из Германии, 17 -из Нидерландов, 15 -из США.…”

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“…Показатели первых двух пунктов относились к α-разнообразию, следующих двухк β-разнообразию, которые, при наличии нескольких породных выборок, характеризовали изменчивость оценок α-разнообразия в пространстве. Методические стороны оценивания рассмотрены в [10,11,16,17,18]. Для анализа полокусных оценок применяли методы традиционной (описательная статистика, парное сравнение средних и медиан, ковариационный анализ) и многомерной статистики (анализ главных компонент, неметрическое многомерное шкалирование, кластерный анализ и анализ Прокруста).…”

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Analysis of locus estimates of allelic diversity of STR markers in a sample of breeding bulls

Kuznetsov

2023

Аграрная наука Евро-Северо-Востока

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Genotypes of the 11 DNA microsatellite loci of 84 bulls of seven breeds were used to evaluate 14 indicators of allelic diversity/differentiation. Traditional and multidimensional statistical methods were applied to the data matrices from the original and transformed estimates (11×14). Estimates of heterozygosity had coefficients of variability of 8-14 %, the number of alleles per locus and indicators of differentiation of breeds at the level of 20-26 %, fixation indices – 38-44 %. Statistically significant Kendall correlations (0.8-1.0) between indicators of allelic richness and heterozygosity, fixation indices, and differentiation indicators were established. The variability of the transformed estimates of diversity/differentiation indicators by loci was in the range of 6-32 %. Including by loci Eth3, Tgla122, Eth225, Bm2113 – 6-12 %, loci Inra23, Tgla126, Eth10 – 15-20 %, loci Tgla227, Sps115, Tgla53, Bm1824 – 28-32 %. The nonparametric Mann-Whitney-Wilcoxon test showed statistically significant differences in the medians of the Eth3 locus with the Bm2113 locus, the Tgla126 locus with the Eth3, Inra23, Tgla122, Eth225, Bm2113, Bm1824, Eth10 loci. The principal component analysis (PCA) identified two components with a total information content of 95,2 %. The first one took into account 59.4 % of the total variance, had the highest loads in intra-breed diversity data and was defined as an «alpha component». The second accounted for 35.8 % of the total variance, had the highest loads in inter-breed differentiation data and was defined as a «beta component». 2D-PCA-ordination showed that a characteristic grouping of loci took place for the analyzed breeds (samples), loci and measures of diversity. Loci Tgla227 and Tgla53 formed group A, group B – loci Tgla122, Eth225, Eth10, group C – loci Inra23, Bm2113 and Bm1824. The loci of the conditional group D (Eth3, Tgla126, Sps115) were defined as «untypical». Validation of ordination was confirmed by calculations on reduced data (dimension 11×7) and the method of non-metric multidimensional scaling (nMDS). The consistency of ordinations according to the Procrust test was 96 % (pperm <0.001). A similar classification of loci was obtained by cluster analysis (UPGMA) with butstrap probabilities of cluster: A – 73, B – 100, C – 73, D – 47 %. The distances and similarity indicators (S) between the profiles of loci and the «true» summary estimates for 11 loci were calculated. Loci Tgla126 and Sps115 had S ≈ 40 %, loci Tgla53 and Bm1824 – at the level of 60 %, loci Inra23, Tgla227 and Bm2113 – 70-75 %, loci Eth3, Tgla122, Eth225 and Eth10 – 84-88 %. The average absolute deviation of the estimates of diversity indicators for the four loci with S≥84 % from the «true» estimates was 3.4 %, for the four loci with S≤60 % – 12.4 %. According to component scores, a general diversity index, γLV, was calculated for each locus. Its correlation with the estimates of the Shannon/Sherwin′s γ-diversity with a 95 % probability value was in the range of 0.73-0.98, Kendall's rank correlation was 0.67 (pvalue = 0.005). The conducted research makes a certain contribution to the expansion of tools for processing molecular genetic data in the analysis of allelic diversity in subdivided populations.

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Analysis of locus estimates of allelic diversity of STR markers in a sample of breeding bulls

Kuznetsov

2023

Аграрная наука Евро-Северо-Востока

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Genetic diversity of today’s and ancestral populations of purebred Kholmogory cattle in the Komi Republic

Matyukov,

Zharikov

2023

Proceedings of the Komi Science Centre of the Ural Division of the Russian Academy of Sciences

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The genealogical information and genetic markers of different types were used to evaluate the genetic diversity of the endangered Kholmogory cattle breed in the Komi Republic. The main genealogical and gene pool of the ancestral population is available in the gene pool farms and the bank of cryopreserved semen of bulls. The effective number of the today’s population is sufficient to prevent the inbreeding from increasing above the acceptable limits for a short time. However, to maintain the genetic diversity for a long time, we need to attain at least a two-fold increase in the effective population number, primarily by increasing the number of seed donors. The use of different types of markers allows to obtain the exhaustive and objective information about the dynamics of the gene pool of the endangered breed.

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Analysis of the diversity of STR-loci in the samples of bulls of Red Scandinavian and Holstein breeds

Kuznetsov

2024

Аграрная наука Евро-Северо-Востока

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Standardized indicators of α- and β-diversity (𝒚′𝒌𝒎) calculated by DNA microsatellites (STR) in samples of bulls of Red Scandinavian (RED, n = 29) and Holstein (HOL, n = 45) breeds (each with three sub-samples) were analyzed using one-two- and multivariate statistics methods. The data represented two 11×7 matrices: objects – 11 STR loci (Eth3, Inra23, Tgla227, Tgla126, Tgla122, Sps115, Eth225, Tgla53, Bm2113, Bm1824, Eth10; No.1-11), variables – three indicators of α-diversity (number of alleles and effective alleles per locus, heterozygosity) and four – β-diversity (indices: fixation by Nei, differentiation by Meirmans-Hedrick, Jost and Shannon-Sherwin). ANOVA, using a fixed-type model, revealed a statistically significant (pvalue< 0.02) effect on the variability of 𝒚′𝒌𝒎 factors «breed» (2 %), «locus» (36.7 %) and their interaction (15.6 %). According to the mixed-type model (the «locus» factor as random), only the interaction effect was statistically significant (25.8 %, pvalue< 0.0001). The probability of a noncoincidence between the numbers of a randomly selected pair of loci from the RED and HOL samples was 31 %. The average Euclidean distance between the two samples, calculated by analogical loci, was 37.8±5.35 %. The Mantel correlation between the matrices of paired interlocus distances in RED and in HOL samples was 0.257±0.130 (pvalue = 0.056). The ordinations of loci and their grouping (structuring) in the space of the two main components of the REL sample and the HOL sample differed (Procrust test: m2 = 0.994, m12 = 0.747, pperm = 0.164, 𝒓𝟐𝑷𝒓𝒐𝒄 = 0.253). Estimates of the distance between samples based on the profiles of the α- and β-diversity of loci did not contradict, in general, the genetic distances calculated by allelic frequencies (29–37 %). To analyze the covariance (commonality) of multivariate RED and HOL sample data, a two-block partial least squares (2B-PLS) method was used. The integrated latent variables (LV) maximized the total square of covariance («squared covar» = 14.3 %), in which 83 % accounted for the first LV with max «weights» in terms of α-diversity (aLV). The second LV accounted for 16.7 % with max «weights» in terms of β-diversity (βLV). The linear relationship between RED and HOL samples for aLV was 0.717 (pvalue = 0.013), for βLV – 0.395 (pvalue = 0.229), averaged – 0.56 (pvalue = 0.025). The commonality (co-dispersion) of the two samples for aLV and βLV was estimated at 25,0–32.5 %. 2B-PLS analysis based on reduced data (only for α-diversity) showed a max «squared covar» of 0.393, in which 99.9 % accounted for the first LV (LV1). According to LV1, the linear relationship between RED and HOL samples was estimated at 0.659 (pvalue = 0.0253), the co-dispersion was 43.4 % (according to aLV it was 51.4 %). The ordinations of loci in the coordinate space of the RED and HOL samples for the complete (αLV) and reduced (LV1) datasets had a good match (Procrust test: m2 = 0.0742, m12 = 0.0728, pperm = 0.001, 𝒓𝟐𝑷𝒓𝒐𝒄 = 0.927). In the structure of the inter-sample covariance, «clumps» of loci with a bootstrap probability of [grouping] 50, 75 and 100 % were distinguished. It can be assumed that the RED and HOL samples had some consistency (congruence) in terms of the α-diversity of the loci of the same name. The extension of the «multivariate» approach to descriptive statistics of α-diversity of 7 breeds of dairy cattle and 11 breeds of pigs showed a fairly good correspondence of the results (differentiation index, PCA-ordination) with those obtained using «traditional» methods (pperm of matching ordinations 0.054 and 0.004). The approaches and methods considered expand the possibilities of population-genetic [and breeding-zootechnical] studies in which multidimensional data sets are the norm, not the exception.

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Information-entropy approach to the analysis of genetic diversity of populations (analytical review)

Cited by 4 publications

References 28 publications

Analysis of locus estimates of allelic diversity of STR markers in a sample of breeding bulls

Analysis of locus estimates of allelic diversity of STR markers in a sample of breeding bulls

Genetic diversity of today’s and ancestral populations of purebred Kholmogory cattle in the Komi Republic

Analysis of the diversity of STR-loci in the samples of bulls of Red Scandinavian and Holstein breeds

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