Genetic distance and classification of domestic animals using genetic markers

Abstract

Genetic distance is used to classify and elucidate the evolutionary relationship between populations, such as species, which have been diverging for a long period. The properties of genetic distance measures in livestock classi®cation have hitherto not been investigated. We used simulation studies to compare the accuracy of eight genetic distance measures to classify recently diverged populations. The effect of varied population sizes from generation to generation were also taken into account. Comparatively better results are obtained from Nei's standard distance with two alleles at each locus and from Nei's D A distance with four alleles at each locus under various conditions. However, the difference in accuracy among distance measures was small and very high correlations were shown. The number of alleles at each locus had a greater effect on accuracy than the number of loci or type of distance measures. It indicates that highly polymorphic markers, such as DNA microsatellite, are powerful tool to improve the accuracy in classi®cation of domestic animals. The six distance measures had a linear relationship with generation number at constant population size. None of the distance measures, however, showed a linear relationship when population size varied. The effect of¯uctuating population size on the average distance was obvious over the ®rst few generations but declined when the number of generations was increased. ZusammenfassungGenetische Distanz und Klassi®zierung von Haustieren mittels genetischer Marker Genetische Distanzen werden verwendet, um evolutiona Ère Beziehungen zwischen Populationen, die vor langer Zeit divergierten, einzuordnen und aufzukla Èren. Die Eigenschaften der hierfu È r verwendeten Maûeinheiten wurden bislang bei Haustieren noch nicht untersucht. Es wurden Simulationsmodelle verwendet, um die Genauigkeit von 8 Distanzmaûen fu È r ku È rzlich divergierte Populationen miteinander zu vergleichen. Dabei wurde der Effekt sich vera Èndernder Populationsgro È ûen miteinbezogen. Die im Vergleich besten Ergebnisse wurden mit Nei's Standard-Distanz mit zwei Allelen je Locus und mit Nei's D A ± Distanz mit 4 Allelen je Locus unter verschiedenen Bedingungen erzielt. Die Unterschiede in der Genauigkeit war zwischen den Distanzmaûen gering und sehr hohe Korrelationen konnten nachgewiesen werden. Die Anzahl der Allele je Locus hatte einen gro È ûeren Ein¯uss auf die Genauigkeit als die Anzahl der Loci oder das Distanzmaû. Dies zeigt, dass hochpolymorphe Marker wie DNA-Mikrosatelliten schlagkra Èftige Instrumente sind, um die Genauigkeit der Klassi®zierung von Haustieren zu verbessern. Die sechs Distanzmaûe hatten bei konstanter Populationsgro È ûe eine lineare Beziehung mit der Generationenzahl. Bei variierender Populationsgro È ûe zeigte allerdings keines der Distanzmaûe eine lineare Beziehung. Der Ein¯uss variierender Populationsgro È ûen auf die durchschnittliche Distanz war wa Èhrend der ersten Generationen offensichtlich, verringerte sich aber bei steigender Generationenzahl.

Study of genetic distances between cattle breeds of Central Europe

“…However, in our populations tight correlations were obtained comparing Nei's, Cavalli-Sforza's and Reynolds, Weyr, Cockerham's distances (data not shown). Similarly, Nagamine and Higuchi (2001) found very high correlations between distances and small differences in accuracy.…”

Genetic relationships among taurine (Bos taurus) and zebu (Bos indicus) populations as revealed by blood groups and blood proteins

“…From a methodological point of view, two main indications can be drawn from the present paper. First, in a recent simulation analysis aiming to compare the accuracy of different genetic distance measures, it was demonstrated that the number of alleles at each locus had a greater effect on accuracy than the number of loci and type of distance measures ( Nagamine and Higuchi 2001). In our paper, almost all the markers used were bi‐allelic, but the high number of considered polymorphisms (43 or 46) could balance the low number of alleles at each locus.…”

“…In fact, the clear separation obtained from the analysis between B. indicus and B. taurus breeds, the strong correspondence between phylogenetic and multivariate analyses, and the fact that the results do not substantially change in considering 43 or 46 markers, well support the statistical approach employed. However, Takezaki and Nei (1996) and Nagamine and Higuchi (2001) demonstrated that increasing the number of the loci involved in the phylogenetic analyses increased noticeably the accuracy of genetic distance estimates in simulation studies, and therefore a high number of polymorphic loci should be always recommended in the phylogenetic studies.…”

Variabilidad genética en ganaderías de lidia mexicanas a partir de la información del registro genealógico

“…Una población subdividida muestra niveles de heterocigosis menores a los esperados, y esa reducción en heterocigosis puede ser utilizada para cuantificar el grado de diferenciación entre sub poblaciones por medio del estadístico F de Wright (Caballero & Toro 2000); además, las distancias genéticas miden la diversidad o grado de diferenciación genética entre poblaciones, ayudan a entender las relaciones existentes (evolutivas o no) y dan una estimación relativa del tiempo que ha pasado desde que las poblaciones se diferenciaron (Nagamine & Higuchi 2001). Con base en lo anterior, los objetivos del presente estudio fueron estimar las distancias genéticas y analizar la posible variación o diferenciación genética a través de ganaderías de lidia mexicanas.…”