Assessment of genetic differentiation of populations by analysis of molecular variance (analytical review)

Kuznetsov, V. M.

doi:10.30766/2072-9081.2021.22.2.167-187

Cited by 7 publications

(4 citation statements)

References 39 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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“…По Data1r для каждого локуса были рассчитаны γLV-оценки и сопоставлены с полокусными оценками γ-разнообразия Шеннона/ Шервина (D'γ) 17 . Использовали непараметрический тест Колмогорова-Смирнова, который проверял любые различия распределений, любых параметров, без конкретизации каких именно.…”

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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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Assessment of genetic diversity and phylogenetic relationships in Black Pied cattle in the Novosibirsk Region using microsatellite markers

2022

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There are currently over a thousand indigenous cattle breeds well adapted to local habitat conditions thanks to their long history of evolution and breeding. Identification of the genetic variations controlling the adaptation of local cattle breeds for their further introduction into the genome of highly productive global breeds is a matter of great relevance. Studying individual populations of the same breed with the use of microsatellite markers makes it possible to assess their genetic diversity, relationships, and breed improvement potential. Although the Black Pied breed is the most common dairy cattle breed in Russia, there are only a few studies on genetic diversity in local Black Pied populations in some Russian regions. The goal of the present study was to analyze the genetic diversity in Black Pied cattle populations in the Novosibirsk Region and compare them with other Russian populations; to identify significantly divergent populations with a view to preserving them under the programs aimed at maintaining the genetic diversity of the domestic Black Pied breed. DNA samples from 4788 animals of the Black Pied breed from six breeding enterprises in the Novosibirsk Region have been studied using 11 microsatellite markers. No significant differences in genetic variability parameters were found between individual populations. Private alleles have been identified in five out of six populations. Five populations have shown inbreeding coefficient values (FIS) below zero, which indicates heterozygosity excess. The population distribution test, principal component analysis, FST and DEST values, cluster analysis, and phylogenetic analysis have revealed two populations genetically distinct from the others. Essentially, the genetic diversity parameters of the six studied Black Pied cattle populations from the Novosibirsk Region show no significant differences from other Russian populations of the breed. Excess heterozygosity is observed in most breeding enterprises, which is a sign of a low inbreeding rate. To maintain the genetic diversity of the Russian Black Pied cattle, we recommend focusing on the two populations with significant genetic distinctions from the others.

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

Kuznetsov

2022

Аграрная наука Евро-Северо-Востока

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The application of information-entropy analysis on real data is shown: 84 bulls of Jersey (n = 10), Ayrshire (n = 10), red Danish (n = 10), red Swedish (n = 9) breeds and Holstein ecotypes of German (n = 13), Dutch (n = 17) and North American (n = 15) breeding genotyped by 11 microsatellite loci. The Shannon information index for the combined breed samples was 1.695, the weighted average for the samples was 1.325, the inter-sample component (SHAP) was 0.370 nits or 21.8 % (all calculations according to GenAlEx 6.502). The total absolute diversity of Shannon was 5.45, averaged by samples – 3.76 effective alleles per locus, between breeds – 1.45 effective samples. The relative estimate of the differentiation of breed samples (D'β) was 36.2 % and was close to the «traditional» estimates for Hedrick, Jost and Ciao. The influence of within samples heterozygosity on SHAP estimates has not been established, but a positive trend of D'β-estimates has been noted. The matrix of paired genetic distances by breeds (D'β) and its 2D projection had a high correspondence with those by GST(NEI)-, FST(W&C)-, G"ST(HED)-, F'ST(W&C)-, DJOST-, DCHAO-measures (RMantel ≥ 0,94). Fixation indices (GST(NEI) and FST(W&C)) should be used to study the evolutionary stories of subdivided populations. To analyze the current structure of the genetic diversity of (sub)populations with an emphasis on dominant allele measures based on heterozygosity (G'ST(HED), F'ST(W&C), DJOST and DCHAO), if necessary, take into account all alleles – the Shannon measure (D'β). In conclusion, a family of Hill power measures of order q = 0, 1, 2 is considered for constructing diversity profiles containing all information about the distribution of alleles in a population.

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Assessment of genetic differentiation of populations by analysis of molecular variance (analytical review)

Cited by 7 publications

References 39 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

Assessment of genetic diversity and phylogenetic relationships in Black Pied cattle in the Novosibirsk Region using microsatellite markers

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

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