PHYLOGENETIC RECONSTRUCTION AND MOLECULAR EVOLUTION ANALYSIS USING HIGH-RESOLUTION GENOMIC DATA

Abstract

The appearance of high-resolution genomic data developed under the impact of next-generation sequencing technologies has greatly contributed to the development of phylogenetic reconstruction and evolution molecular studies. This paper gives an integrative method of genome-wide inference of phylogenetic studies on evolutionary interpretation utilizing high-density single nucleotide polymorphism (SNP) datasets. The whole-genome sequencing data of several samples were put to an overall computation pipeline, consisting of quality control, reference-based alignment, and variant calling using GATK. The total high-confidence SNPs were discovered and utilized in the phylogenetic reconstruction with the maximum likelihood techniques applied in IQ-TREE that was strongly supported with bootstrap. The Molecular evolution was measured by adoption of codon based substitution models to determine the rate of synonymous and non synonymous substitutions so that they could identify the genes under the selective pressure. The results of the analysis showed that most of the genomic regions were subjected to intense purifying pressure with some of the genes representing the indicators of positive selection related to essential functional pathways. ANNOTAV functional annotation also provided more evidence of the participation of those genes in important biological events, such as metabolic regulation and cell signaling. The findings show that the combination of phylogenomic reconstruction and molecular evolution analysis improves the research and interpretation of evolutionary relations. The framework is a scalable and reproducible method of exploring evolutionary genetic diversity and adaptive evolution in complex genomic samples.