Phylogenomics — principles, opportunities and pitfalls of big‐data phylogenetics

作者：Andrew Donovan Young, Jéssica P. Gillung · 发表于：Systematic Entomology · 年份：2019 · DOI：10.1111/syen.12406 · 被引用次数：208 · 研究领域：Genomics and Phylogenetic Studies、Genetic diversity and population structure、Evolution and Paleontology Studies

Phylogenetics is the science of reconstructing the evolutionary history of life on Earth. Traditionally, phylogenies were constructed using morphological data only, but the introduction of Sanger sequencing and PCR in the late 1970s enabled genetic information to be incorporated into phylogenetic analyses. Early phylogenetic studies employing multilocus analyses contributed greatly to our knowledge of phylogenetic history and challenged some well-established views of the relationships among many groups of plants and animals. Since the publication of these pioneering studies, significant methodological advances in both sequencing and analytical techniques have been made, and molecular phylogenies are now broadly accepted to represent robust hypotheses of organismal relationships. Next-generation sequencing techniques, developed in the mid-2000s, revolutionized DNA sequencing and led to a dramatic reduction in sequencing cost per nucleotide and a sharp increase in data generation speed. As a result, the generation of unprecedented amounts of sequence data for both model and nonmodel organisms has become affordable. This development has transformed the field of molecular phylogenetics into phylogenomics—where genome-scale data are obtained from multiple samples at once at a much reduced cost (Mardis, 2011). The phylogenomic pipeline can be very complex, presenting an overwhelming array of methodologies available for the acquisition, manipulation, analysis and interpretation of m...