Popülasyon Genomiği: Temel Kavramlar ve Yöntemler
Özet
Bu bölüm, popülasyon genomisinin temel kavramlarını, veri türlerini ve analiz yöntemlerini kapsamlı ancak uygulamaya dönük bir yaklaşımla tanıtmaktadır. Öncelikle SNP, STR, CNV, indel, yapısal varyant ve haplotip gibi genomik veri türleri ile PLINK ve VCF başta olmak üzere yaygın veri formatları açıklanmaktadır. Güvenilir analiz sonuçları elde etmek amacıyla kalite kontrolü, filtreleme, eksik genotiplerin tamamlanması ve format dönüşümü süreçleri ele alınmaktadır. Bölümde ayrıca Temel Bileşenler Analizi, ortak soy ve karışma analizi, genetik çeşitlilik ölçütleri, FST, AMOVA, genetik uzaklık, akrabalık ve genomik ilişki matrisleri açıklanmaktadır. Doğal ve yapay seçilimin genomda bıraktığı izlerin belirlenmesine yönelik Tajima’s D, Fay-Wu’s H, EHH, iHS ve XP-EHH gibi yöntemlere de yer verilmektedir. Son olarak PLINK, GATK, bcftools, ADMIXTURE, STRUCTURE ve çeşitli R paketleri kullanılarak genomik analizlerin biyoenformatik iş akışı sunulmaktadır. Bölüm; tarım, hayvan ve bitki ıslahı, tıp, biyoçeşitliliğin korunması ve adaptasyon araştırmaları için temel bir başvuru niteliğindedir.
This chapter introduces the fundamental concepts, data types, and analytical methods of population genomics through a comprehensive yet application-oriented framework. It first describes genomic data types—including SNPs, STRs, CNVs, indels, structural variants, and haplotypes—and commonly used formats such as PLINK and VCF. To ensure reliable results, the chapter explains quality control, filtering, genotype imputation, and data-format conversion procedures. It then presents major approaches for investigating population structure and evolutionary processes, including Principal Component Analysis, ancestry and admixture analysis, genetic diversity metrics, FST, AMOVA, genetic distance, kinship, and genomic relationship matrices. Methods for detecting genomic signatures of natural and artificial selection, such as Tajima’s D, Fay and Wu’s H, EHH, iHS, and XP-EHH, are also discussed. Finally, the chapter outlines a practical bioinformatics workflow using PLINK, GATK, bcftools, ADMIXTURE, STRUCTURE, and R packages. It provides a foundational resource for studies in agriculture, animal and plant breeding, medicine, biodiversity conservation, and adaptation.
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