Новая программа для анализа субструктуры популяции

На ресурсе Bioarxiv опубликован препринт статьи, описывающей новую программу для анализа предковых компонентов в изучаемых геномах.  Программа называется Ohana (Linuxовские исходники доступны на Github).

Программа представляет собой дальнейшее развитие парадигмы, использованной при создании программ подобного рода, в том числе и популярных Admixture/STRUCTURE.

Что же именно представляет собой программа Ohana:

Мотивация:  методы выявления генетической cтруктуры популяции часто используются в процентной классификации (доли различных компонентов происхождения) отдельных образцов (геномов) в выборке популяции.
Вклад: Мы вводим новый алгоритм оптимизации классической модели структуры в рамках максимального  правдоподобия. Используя анализ реальных данных, мы показываем, что новый алгоритм оптимизации находит более высокие значения оценки правдоподобия, в сравнении с стандартными методами,   за то же самое время вычислений. Мы также представляем новый метод оценки деревьев популяций предковых компонентов с использованием гауссовой аппроксимации. Используя модель коалесценции популяций,  мы моделируем  эволюцию популяций в виде дерева, а затем исследуем адекватность модели структуры и гауссовской аппроксимации в  правильной идентификации предковых  компонентов родословной и вывода правильной типологии дерева популяций. В большинстве случаев предковые компоненты выводятся правильно, хотя очевидно, что  размер выборки и количество времени, прошедшего с момента смешивания предковых компонентов могут влиять на статистическую достоверность выводов. Вместе с этим, популярная гауссовская аппроксимация  работает гораздо хуже в случае с длинными ветвями популяционного дерева, хотя сама топология дерева была определена правильно во всех рассматриваемых сценариях. Новые методы реализованы средствами языка C++  вместе с соответствующими средствами визуализации в программном пакете Ohana.

Судя по описанию, метод явно продвинут в сравнении с Admixture, и поэтому я решил протестировать программу на своих данных. Поскольку задачей опыта являлась только проверка быстродействия и эффективности программы, я ограничился лишь малым числом снипов (около 1000 снипов) и небольшим числом итерационных шагов. Ниже таблица значений параметра максимальной правдоподобности для разных шагов:

step global-lle local-lle lle-ratio
21 -2.6833044517734939e+00 +2.2770091451382113e-01 +5.8220107325746300e+00
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Поскольку это всего лишь тест, то я особо не стремился определить ни правильность определенных предковых 8 компонентов, ни их географический ареал распространения.
Тем не менее,  с наглядной точки зрения, дерево компонентов выглядит красиво (заметен значительный генетический дрейф 8-ой предковой популяции):

FST древо предковых популяций

 

Не менее интересна составленная самой программой столбиковая диаграмма распределения значений компонентов для каждого индивида в моей выборке

q-bar-chart

Поскольку программа мне понравилась, я постараюсь задействовать ее в одном из своих будущих экспериментов

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