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<article article-type="research-article" dtd-version="1.3" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xml:lang="ru"><front><journal-meta><journal-id journal-id-type="publisher-id">vavilov</journal-id><journal-title-group><journal-title xml:lang="ru">Вавиловский журнал генетики и селекции</journal-title><trans-title-group xml:lang="en"><trans-title>Vavilov Journal of Genetics and Breeding</trans-title></trans-title-group></journal-title-group><issn pub-type="epub">2500-3259</issn><publisher><publisher-name>Institute of Cytology and Genetics of Siberian Branch of the RAS</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="doi">10.18699/VJ16.153</article-id><article-id custom-type="elpub" pub-id-type="custom">vavilov-615</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject></subj-group><subj-group subj-group-type="section-heading" xml:lang="ru"><subject>Филогенетика и эволюция</subject></subj-group><subj-group subj-group-type="section-heading" xml:lang="en"><subject>Phylogenetics and evolution</subject></subj-group></article-categories><title-group><article-title>Комбинирование и оценка конгруэнтности филогенетических сигналов от нескольких генов с помощью геометрического подхода</article-title><trans-title-group xml:lang="en"><trans-title>Combining and congruence evaluation of phylogenetic signals from different genes based on geometric approach</trans-title></trans-title-group></title-group><contrib-group><contrib contrib-type="author" corresp="yes"><name-alternatives><name name-style="eastern" xml:lang="ru"><surname>Ефимов</surname><given-names>В. М.</given-names></name><name name-style="western" xml:lang="en"><surname>Efimov</surname><given-names>V. M.</given-names></name></name-alternatives><bio xml:lang="ru"><p>Новосибирск;</p><p>Томск</p></bio><bio xml:lang="en"><p>Novosibirsk;</p><p>Tomsk</p></bio><xref ref-type="aff" rid="aff-1"/></contrib><contrib contrib-type="author" corresp="yes"><name-alternatives><name name-style="eastern" xml:lang="ru"><surname>Ковалева</surname><given-names>В. Ю.</given-names></name><name name-style="western" xml:lang="en"><surname>Kovaleva</surname><given-names>V. Yu.</given-names></name></name-alternatives><bio xml:lang="ru"><p>Новосибирск</p></bio><bio xml:lang="en"><p>Novosibirsk</p></bio><xref ref-type="aff" rid="aff-2"/></contrib><contrib contrib-type="author" corresp="yes"><name-alternatives><name name-style="eastern" xml:lang="ru"><surname>Литвинов</surname><given-names>Ю. Н.</given-names></name><name name-style="western" xml:lang="en"><surname>Litvinov</surname><given-names>Yu. N.</given-names></name></name-alternatives><bio xml:lang="ru"><p>Новосибирск</p></bio><bio xml:lang="en"><p>Novosibirsk</p></bio><xref ref-type="aff" rid="aff-2"/></contrib></contrib-group><aff-alternatives id="aff-1"><aff xml:lang="ru">Федеральное государственное бюджетное учреждение науки «Федеральный исследовательский центр Институт цитологии и генетики&#13;
Сибирского отделения Российской академии наук»;&#13;
Федеральное государственное автономное образовательное учреждение высшего образования «Новосибирский национальный исследовательский&#13;
государственный университет»;&#13;
Федеральное государственное автономное образовательное учреждение высшего образования «Национальный исследовательский Томский&#13;
государственный университет»<country>Россия</country></aff><aff xml:lang="en">Institute of Cytology and Genetics SB RAS;&#13;
Novosibirsk State University;&#13;
Tomsk State University<country>Russian Federation</country></aff></aff-alternatives><aff-alternatives id="aff-2"><aff xml:lang="ru">Федеральное государственное бюджетное учреждение науки Институт систематики и экологии животных Сибирского отделения Российской&#13;
академии наук<country>Россия</country></aff><aff xml:lang="en">Institute of Systematics and Ecology of Animals SB RAS<country>Russian Federation</country></aff></aff-alternatives><pub-date pub-type="collection"><year>2016</year></pub-date><pub-date pub-type="epub"><day>21</day><month>06</month><year>2016</year></pub-date><volume>20</volume><issue>6</issue><fpage>816</fpage><lpage>822</lpage><permissions><copyright-statement>Copyright &amp;#x00A9; Ефимов В.М., Ковалева В.Ю., Литвинов Ю.Н., 2017</copyright-statement><copyright-year>2017</copyright-year><copyright-holder xml:lang="ru">Ефимов В.М., Ковалева В.Ю., Литвинов Ю.Н.</copyright-holder><copyright-holder xml:lang="en">Efimov V.M., Kovaleva V.Y., Litvinov Y.N.</copyright-holder><license license-type="creative-commons-attribution" xlink:href="https://creativecommons.org/licenses/by/4.0/" xlink:type="simple"><license-p>This work is licensed under a Creative Commons Attribution 4.0 License.</license-p></license></permissions><self-uri xlink:href="https://vavilov.elpub.ru/jour/article/view/615">https://vavilov.elpub.ru/jour/article/view/615</self-uri><abstract><p>Обсуждаются возможности недавно предложенного нами нового алгоритма (DJ-метода) для анализа конгруэнтности и комбинирования молекулярно-генетических данных на основе матриц евклидовых расстояний. Этот подход назван геометрическим, поскольку евклидовы дистанции удовлетворяют аксиомам метрики, что обеспечивает возможность помещения множества точек, представляющих последовательности, в некоторое геометрическое пространство без искажения взаимных расстояний и наделения точек этого множества координатами в этом пространстве. Геометричность евклидовых расстояний позволяет применять к молекулярным данным весь арсенал методов многомерного анализа, что является актуальным для исследования соотношения внутри- и межвидовой изменчивости, вычисления центроидов таксонов и расстояний между ними, визуализации возможных направлений эволюции, комбинирования и оценки конгруэнтности филогенетических сигналов, относящихся к разным генам и даже к разным системам признаков. DJ-метод использован для оценки конгруэнтности и комбинирования филогенетических сигналов, получаемых от нескольких генов. Анализировались более 1500 нуклеотидных последовательностей двух ядерных (apoB, brca1) и двух митохондриальных (co1, cytb) генов 15 палеарктических и неарктических видов землероек-бурозубок рода Sorex (Soricidae, Eulipotyphla). Для каждого гена все его последовательности представлялись множеством точек в евклидовом пространстве. Для множества точек, относящихся к одному виду, вычислялся его центроид в этом же пространстве. Для каждого гена вычислялась матрица евклидовых расстояний между центроидами видов. Для оценки попарного сходства (конгруэнтности) матриц межвидовых расстояний применен тест Мантеля. Конгруэнтность генов яДНК составила 0.961, мтДНК – 0.748. Все матрицы межвидовых расстояний через взвешивание объединены в единую матрицу. По ней методом главных координат для всех видов построено единое пространство. В объединенном генетическом пространстве проявилось несколько направлений межвидовой изменчивости, отражающих разные по масштабу эволюционные события. Кроме того, по объединенной матрице межвидовых расстояний построено дерево, которое хорошо согласуется с принятой на сегодня зоологической систематикой. Это подтверждает работоспособность предложенного нами метода.</p></abstract><trans-abstract xml:lang="en"><p>A new Euclidean distance based algorithm is used for analysis of congruence and combining molecular genetic data. This approach is called geometric, since Euclidean distance satisfies all metric axioms and the points representing the sequences can be placed in a geometric space without distorting the mutual distances and can be endowed with the coordinates in this space. Geometricness of Euclidean distances allows to apply to molecular data methods of multivariate analysis, which are relevant for intra- and interspecies variability investigating, visualization of possible directions of evolution, combining data and evaluation of the congruence of phylogenetic signals. The algorithm is used for the analysis of more than 1500 nucleotide sequences of two nuclear (apoB, brca1) and two mitochondrial (co1, cytb) genes of 15 Palaearctic and Nearctic shrews species of genus Sorex (Soricidae, Eulipotyphla). All sequences of each gene are represented as a set of points in Euclidean space. Centroids of a set of points belonging to the same species are calculated. The matrix of Euclidean distances between the species centroids is calculated for each gene. Mantel test is applied to estimate pairwise similarity (congruence) of interspecies distances matrices relating to different genes. nDNA genes congruence is equal 0.961, mtDNA – 0.748. All matrices of the interspecies distances are combined into a joint matrix by weighing. Joint genetic space for all species is built by principal coordinate method from the joint matrix. Several variability directions reflecting evolutionary events of different scale are visualized in a joint genetic space. In addition, the joint matrix of interspecies distances is used for building a phylogenetic tree which is consistent with the zoological systematics accepted for today. This confirms the efficiency of our proposed method.</p></trans-abstract><kwd-group xml:lang="ru"><kwd>Sorex</kwd><kwd>мтДНК</kwd><kwd>яДНК</kwd><kwd>DJ-метод</kwd><kwd>филогенетика</kwd><kwd>евклидово пространство</kwd></kwd-group><kwd-group xml:lang="en"><kwd>Sorex</kwd><kwd>mtDNA</kwd><kwd>nuclear DNA</kwd><kwd>DJ-method</kwd><kwd>Phylogenetics</kwd><kwd>Euclidean space</kwd></kwd-group><funding-group xml:lang="ru"><funding-statement>СО РАН, РФФИ</funding-statement></funding-group></article-meta></front><back><ref-list><title>References</title><ref id="cit1"><label>1</label><citation-alternatives><mixed-citation xml:lang="ru">Гречко В.В. 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