STUDYING ANCIENT LIVESTOCK-ORIGINATED DNA AND BIOINFORMATICS

Hosseini, Hamidreza; Maghsoudi, Ali; Erfanmanesh, Parastou

doi:10.22034/jsbs.2025.501869.1068

STUDYING ANCIENT LIVESTOCK-ORIGINATED DNA AND BIOINFORMATICS

Document Type : Original Research Article

Authors

Hamidreza Hosseini ¹

Ali Maghsoudi ²

Parastou Erfanmanesh ³

¹ Researcher and lecturer in the Department of Computer and Bioinformatics, University of Zabol, Zabol, Iran

² Department of Animal Science, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran

³ Biology Laboratory of the Research Institute for Protection and Restoration of Historical- Cultural Monuments Research

10.22034/jsbs.2025.501869.1068

Abstract

The study of ancient DNA (aDNA) is a rapidly evolving field within bioinformatics, offering valuable insights into the genetic diversity, migration, and evolution of past populations. Advances in high-throughput sequencing technologies have enabled the retrieval of genomic-scale data from archaeological and historical specimens, including subfossil remains. Bioinformatics tools are essential for processing this data, addressing challenges posed by the degradation of aDNA and recovering useful genetic and even epigenetic information. Key bioinformatics applications include sequence alignment, phylogenetic analysis, and identifying genetic relationships between extinct and extant species. These studies have broad interdisciplinary implications in fields such as archaeology, anthropology, human genetics, ecology, and evolutionary biology. aDNA research has contributed to understanding ancient diets, domestication processes, and microbiomes, with samples extracted from sediments, ice cores, and other environmental sources. However, challenges remain: aDNA is often fragmented and chemically altered, and a high proportion of sequenced DNA belongs to non-target species. Effective separation and identification of target DNA rely on tools like BLAST, Bowtie2, and BWA, and on microbial databases, despite their limitations. Furthermore, the preservation conditions, such as temperature, significantly affect DNA survival. Fossils like those of mammoths or Aurochs offer valuable material for genetic studies, though phylogenetic isolation, as seen in saber-toothed cats, can hinder comparative analysis. Nevertheless, ongoing technological progress continues to refine the understanding of ancient genomes.

Keywords

Bioinformatics

Ancient DNA

Alignment

Computational Biology

aDNA Sequencing

چکیده: مطالعه‌ DNA باستانی (aDNA) یکی از حوزه‌های نوظهور و پویای زیست‌اطلاعاتی (بیوانفورماتیک) است که بینش‌های ارزشمندی درباره‌ی تنوع ژنتیکی، مهاجرت و فرگشت جمعیت‌های گذشته فراهم می‌کند. پیشرفت در فناوری‌های تعیین توالی پرظرفیت (high-throughput) امکان بازیابی داده‌های ژنومی در مقیاس وسیع از نمونه‌های باستان‌شناسی و تاریخی، از جمله بقایای نیمه‌فسیلی را فراهم کرده است. ابزارهای بیوانفورماتیکی نقش اساسی در پردازش این داده‌ها، رفع چالش‌های ناشی از تخریب DNA باستانی و بازیابی اطلاعات ژنتیکی و حتی اپی‌ژنتیکی ایفا می‌کنند. کاربردهای کلیدی بیوانفورماتیک شامل هم‌ترازی توالی‌ها، تحلیل‌های تبارشناختی و شناسایی روابط ژنتیکی میان گونه‌های منقرض‌شده و موجودات زنده امروزی است. این مطالعات پیامدهای بین‌رشته‌ای گسترده‌ای در حوزه‌هایی چون باستان‌شناسی، انسان‌شناسی، ژنتیک انسانی، بوم‌شناسی و زیست‌شناسی فرگشتی دارند. پژوهش بر روی aDNA به درک رژیم‌های غذایی باستانی، فرآیند اهلی‌سازی و میکروبیوم‌های کهن کمک کرده است و نمونه‌هایی از رسوبات، هسته‌های یخی و منابع محیطی دیگر استخراج می‌شوند. با این حال، چالش‌هایی نیز وجود دارد: aDNA معمولاً قطعه‌قطعه و دچار آسیب شیمیایی است و بخش زیادی از DNA تعیین توالی‌شده متعلق به گونه‌های غیرهدف است. شناسایی و جداسازی مؤثر DNA هدف نیازمند ابزارهایی چون BLAST،Bowtie2 و BWA و استفاده از پایگاه‌های داده میکروبی، با وجود محدودیت‌های آن‌هاست. همچنین، شرایط نگهداری مانند دما نقش مهمی در بقای DNA دارد. فسیل‌هایی مانند ماموت‌ها یا گونه‌ منقرض‌شده‌ اوروک (Aurochs) مواد ارزشمندی برای مطالعات ژنتیکی فراهم می‌کنند، هرچند که انزوای تبارشناختی در برخی گونه‌ها مانند ببر دندان‌خنجری، تحلیل تطبیقی را دشوار می‌سازد. با این وجود، پیشرفت‌های فناورانه به بهبود مستمر درک ما از ژنوم‌های باستانی کمک می‌کنند.

کلیدواژه: بیوانفورماتیک، DNA باستانی، هم‌ترازی، زیست‌شناسی محاسباتی، تعیین توالی aDNA.

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