GEOMETRIC PROPERTIES OF EVOLUTIONARY DISTANCES
One way to study the variability of biologic objects is their geometrization: the objects are presented by points in a multidimensional space in such a way that the distances between the points would be best consistent with the dissimilarities between objects. If the dissimilarities between the obje...
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| Format: | Article |
| Language: | English |
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Siberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and Breeders
2015-01-01
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| Series: | Вавиловский журнал генетики и селекции |
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| Online Access: | https://vavilov.elpub.ru/jour/article/view/195 |
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| author | V. M. Efimov M. A. Melchakova V. Yu. Kovaleva |
| author_facet | V. M. Efimov M. A. Melchakova V. Yu. Kovaleva |
| author_sort | V. M. Efimov |
| collection | DOAJ |
| description | One way to study the variability of biologic objects is their geometrization: the objects are presented by points in a multidimensional space in such a way that the distances between the points would be best consistent with the dissimilarities between objects. If the dissimilarities between the objects are Euclidean distances, this task (up to translation, rotation and reflection) is solved by metric scaling. We consider the metric properties of some well-known evolutionary distances of nucleotide sequences. It is shown that the Jukes-Cantor and Kimura distances are not metrics. We introduce a new Kimura distance analog, the PQdistance. It is shown that the p and PQ distances are the squares of Euclidean metrics named Ep-distance and EPQ-distance, respectively. The applicability of the EPQ distance is illustrated by the example of a cytochrome b sequence set of 12 rodent species from West Siberia and Altai, taken from the GenBank, and compared with the results of the use of the LogDet-distance. |
| format | Article |
| id | doaj-art-0b65aabf752242698b4f9746f16fb1d5 |
| institution | Kabale University |
| issn | 2500-3259 |
| language | English |
| publishDate | 2015-01-01 |
| publisher | Siberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and Breeders |
| record_format | Article |
| series | Вавиловский журнал генетики и селекции |
| spelling | doaj-art-0b65aabf752242698b4f9746f16fb1d52025-02-01T09:58:00ZengSiberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and BreedersВавиловский журнал генетики и селекции2500-32592015-01-01174/1714723179GEOMETRIC PROPERTIES OF EVOLUTIONARY DISTANCESV. M. Efimov0M. A. Melchakova1V. Yu. Kovaleva2Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia Institute of Systematics and Ecology of Animals SB RAS, Novosibirsk, Russia Tomsk National Research State University, Tomsk, RussiaNovosibirsk National Research State University, Novosibirsk, RussiaInstitute of Systematics and Ecology of Animals SB RAS, Novosibirsk, RussiaOne way to study the variability of biologic objects is their geometrization: the objects are presented by points in a multidimensional space in such a way that the distances between the points would be best consistent with the dissimilarities between objects. If the dissimilarities between the objects are Euclidean distances, this task (up to translation, rotation and reflection) is solved by metric scaling. We consider the metric properties of some well-known evolutionary distances of nucleotide sequences. It is shown that the Jukes-Cantor and Kimura distances are not metrics. We introduce a new Kimura distance analog, the PQdistance. It is shown that the p and PQ distances are the squares of Euclidean metrics named Ep-distance and EPQ-distance, respectively. The applicability of the EPQ distance is illustrated by the example of a cytochrome b sequence set of 12 rodent species from West Siberia and Altai, taken from the GenBank, and compared with the results of the use of the LogDet-distance.https://vavilov.elpub.ru/jour/article/view/195nucleotide sequencesevolution modelsphylogenetic reconstructionsgenetic distancesgeometrizationzoological systematics |
| spellingShingle | V. M. Efimov M. A. Melchakova V. Yu. Kovaleva GEOMETRIC PROPERTIES OF EVOLUTIONARY DISTANCES Вавиловский журнал генетики и селекции nucleotide sequences evolution models phylogenetic reconstructions genetic distances geometrization zoological systematics |
| title | GEOMETRIC PROPERTIES OF EVOLUTIONARY DISTANCES |
| title_full | GEOMETRIC PROPERTIES OF EVOLUTIONARY DISTANCES |
| title_fullStr | GEOMETRIC PROPERTIES OF EVOLUTIONARY DISTANCES |
| title_full_unstemmed | GEOMETRIC PROPERTIES OF EVOLUTIONARY DISTANCES |
| title_short | GEOMETRIC PROPERTIES OF EVOLUTIONARY DISTANCES |
| title_sort | geometric properties of evolutionary distances |
| topic | nucleotide sequences evolution models phylogenetic reconstructions genetic distances geometrization zoological systematics |
| url | https://vavilov.elpub.ru/jour/article/view/195 |
| work_keys_str_mv | AT vmefimov geometricpropertiesofevolutionarydistances AT mamelchakova geometricpropertiesofevolutionarydistances AT vyukovaleva geometricpropertiesofevolutionarydistances |