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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/vjgb-25-50</article-id><article-id custom-type="elpub" pub-id-type="custom">vavilov-4613</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>БИОИНФОРМАТИКА И СИСТЕМНАЯ БИОЛОГИЯ</subject></subj-group><subj-group subj-group-type="section-heading" xml:lang="en"><subject>BIOINFORMATICS AND SYSTEMS BIOLOGY</subject></subj-group></article-categories><title-group><article-title>Применение метода глубокого обучения  для оценки соотношения репродуктивных режимов в частично клональной популяции</article-title><trans-title-group xml:lang="en"><trans-title>Deep learning approach to the estimation of the ratio  of reproductive modes in a partially clonal population</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>Николаева</surname><given-names>Т. А.</given-names></name><name name-style="western" xml:lang="en"><surname>Nikolaeva</surname><given-names>T. A.</given-names></name></name-alternatives><bio xml:lang="ru"><p>Иркутск</p><p>Новосибирск</p></bio><bio xml:lang="en"><p>Irkutsk</p><p>Novosibirsk</p></bio><email xlink:type="simple">t.maryanovskaya@alumni.nsu.ru</email><xref ref-type="aff" rid="aff-1"/></contrib><contrib contrib-type="author" corresp="yes"><name-alternatives><name name-style="eastern" xml:lang="ru"><surname>Порошина</surname><given-names>А. А.</given-names></name><name name-style="western" xml:lang="en"><surname>Poroshina</surname><given-names>A. A.</given-names></name></name-alternatives><bio xml:lang="ru"><p>Иркутск</p></bio><bio xml:lang="en"><p>Irkutsk</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>Щербаков</surname><given-names>Д. Ю.</given-names></name><name name-style="western" xml:lang="en"><surname>Sherbakov</surname><given-names>D. Yu.</given-names></name></name-alternatives><bio xml:lang="ru"><p>Иркутск</p><p>Новосибирск</p></bio><bio xml:lang="en"><p>Irkutsk</p><p>Novosibirsk</p></bio><xref ref-type="aff" rid="aff-1"/></contrib></contrib-group><aff-alternatives id="aff-1"><aff xml:lang="ru">Лимнологический институт Сибирского отделения Российской академии наук; Новосибирский национальный исследовательский государственный университет<country>Россия</country></aff><aff xml:lang="en">Limnological Institute of the Siberian Branch of the Russian Academy of Sciences; Novosibirsk State University<country>Russian Federation</country></aff></aff-alternatives><aff-alternatives id="aff-2"><aff xml:lang="ru">Лимнологический институт Сибирского отделения Российской академии наук<country>Россия</country></aff><aff xml:lang="en">Limnological Institute of the Siberian Branch of the Russian Academy of Sciences<country>Russian Federation</country></aff></aff-alternatives><pub-date pub-type="collection"><year>2025</year></pub-date><pub-date pub-type="epub"><day>03</day><month>06</month><year>2025</year></pub-date><volume>29</volume><issue>3</issue><elocation-id>467­-473</elocation-id><permissions><copyright-statement>Copyright &amp;#x00A9; Николаева Т.А., Порошина А.А., Щербаков Д.Ю., 2025</copyright-statement><copyright-year>2025</copyright-year><copyright-holder xml:lang="ru">Николаева Т.А., Порошина А.А., Щербаков Д.Ю.</copyright-holder><copyright-holder xml:lang="en">Nikolaeva T.A., Poroshina A.A., Sherbakov D.Y.</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/4613">https://vavilov.elpub.ru/jour/article/view/4613</self-uri><abstract><p>Генетическое разнообразие биологических объектов, таких как популяции, виды и сообщества, является важнейшим источником информации для понимания их структуры и функционирования. Однако многие экологические и эволюционные проблемы возникают из­за того, что наборы данных содержат относительно небольшое количество выборок, что затрудняет использование традиционных методов анализа. В связи c этим наше исследование предлагает новый подход, основанный на глубоком обучении, для решения одной из самых актуальных задач эволюционной биологии – поиска баланса между половым и бесполым размножением. Половое размножение часто приводит к нарушению выгодных комбинаций генов, которые были отобраны в процессе эволюции. С другой стороны, бесполое размножение позволяет организмам быстрее размножаться без участия самцов, эффективно поддерживая полезные генотипы. Исследование посвящено изучению закономерностей сосуществования полового и бесполого размножения в рамках одного вида. Мы разработали специальную сверточную модель нейронной сети, предназначенную для анализа динамики популяций, которые демонстрируют смешанные репродуктивные стратегии в изменяющихся условиях. Эта модель позволяет оценить долю потомков репродуктивного размножения, если эта доля остается постоянной в течение достаточного периода времени, в популяциях, состоящих из постоянного числа организмов, с использованием мультиаллельных признаков, таких как микросателлитные повторы. Результаты показали, что модель с точностью 0.99 оценивает соотношение репродуктивных режимов, эффективно справляясь с трудностями, связанными с небольшими выборками. Более того, когда размерность обучающего набора данных соответствует фактическим данным, модель быстрее достигает минимальной ошибки, что подчеркивает важность подбора структуры набора данных для точности предсказаний. Эта работа вносит значительный вклад в понимание динамики репродуктивной стратегии в эволюционной биологии, демонстрируя потенциал глубокого обучения для улучшения анализа генетических данных. Наши результаты открывают двери для будущих исследований, посвященных тонкостям генетического разнообразия и способам размножения в изменчивых экологических условиях, подчеркивая важность современных вычислительных методов в эволюционных исследованиях. </p></abstract><trans-abstract xml:lang="en"><p>Genetic diversity among biological entities, including populations, species, and communities, serves as a fundamental source of information for understanding their structure and functioning. However, many ecological and evolutionary problems arise from limited and complex datasets, complicating traditional analytical approaches. In this context, our study applies a deep learning­based approach to address a crucial question in evolutionary biology: the balance  between sexual and asexual reproduction. Sexual reproduction often disrupts advantageous gene combinations favored by selection, whereas asexual reproduction allows faster proliferation without the need for males, effectively maintaining beneficial genotypes. This research focuses on exploring the coexistence patterns of sexual and asexual reproduction within a single species. We developed a convolutional neural network model specifically designed to analyze the dynamics of populations exhibiting mixed reproductive strategies within changing environments. The model developed here allows one to estimate the ratio of population members who originate from sexual reproduction to the clonal organisms produced by parthenogenetic females. This model assumes the reproductive ratio remains constant over time in populations with dual reproductive strategies and stable population sizes. The approach proposed is suitable for neutral multiallelic marker traits such as microsatellite repeats. Our results demonstrate that the model estimates the ratio of reproductive modes with an accuracy as high as 0.99, effectively handling the complexities posed by small sample sizes. When the training dataset’s dimensionality aligns with the actual data, the model converges to the minimum error much faster, highlighting the significance of dataset design in predictive performance. This work contributes to the understanding of reproductive strategy dynamics in evolutionary biology, showcasing the potential of deep learning to enhance genetic data analysis. Our findings pave the way for future research examining the nuances of genetic diversity and reproductive modes in fluctuating ecological contexts, emphasizing the importance of advanced computational methods in evolutionary studies.</p></trans-abstract><kwd-group xml:lang="ru"><kwd>глубокое обучение</kwd><kwd>сверточная нейронная сеть (CNN)</kwd><kwd>равновесие Харди–Вайнберга</kwd><kwd>частично клональная популяция</kwd><kwd>микросателлиты</kwd></kwd-group><kwd-group xml:lang="en"><kwd>deep learning</kwd><kwd>convolutional neural network (CNN)</kwd><kwd>Hardy–Weinberg equilibrium</kwd><kwd>partially clonal population</kwd><kwd>microsatellites</kwd></kwd-group><funding-group xml:lang="en"><funding-statement>The study was carried out within the framework of the state budget theme No. 0279­2021­0010 “Genetics of  Baikal organism communities: the gene pool structure, conservation strategies”. Acknowledgements. 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