Phylogenomics

A Primer

Rob DeSalle, Michael Tessler, Jeffrey Rosenfeld

• Publisher: CRC Press
• Year: 2020
• ISBN:
  9781000080391
• Edition: 2
• Topic: Ciencia de la computación
• Subtopic: Ciencias computacionales general

Phylogenomics: A Primer, Second Edition is for advanced undergraduate and graduate biology students studying molecular biology, comparative biology, evolution, genomics, and biodiversity. This book explains the essential concepts underlying the storage and manipulation of genomics level data, construction of phylogenetic trees, population genetics, natural selection, the tree of life, DNA barcoding, and metagenomics. The inclusion of problem-solving exercises in each chapter provides students with a solid grasp of the important molecular and evolutionary questions facing modern biologists as well as the tools needed to answer them.

Section IV

Population Genomics

Chapters 18–21

The transformation of population genetics by the use of DNA sequence information, the detection of natural selection on genes derived from genomic data, and the application of genome-level approaches to population genetics are essential to the understanding of natural populations in an evolutionary context. Chapters 18 and 19 focuses on basic population genetics and this endeavor has been transformed from single locus thinking to genome level thinking and is followed by a discussion of the novel methodology developed over the past decade to accommodate genome level information. Perhaps one of the best examples of natural selection in nature comes from close examination of how DNA sequences evolve over time. Because of the way the genetic machinery in organisms on our planet works, it is possible to detect changes in sequences that are the result of positive selection, neutral selection and negative selection. This topic is incredibly important in modern phylogenetics and we devote two chapters to it (Chapters 20 and 21). The first of these chapters (Chapter 20) demonstrates the theory behind detecting natural selection using genome level information. Chapter 21 discusses the impact of this way of analyzing genomic data in modern biology.

	CHAPTER
Population Genetics and Genomes	18

Population genetics has a long history, as it was developed along with the rediscovery of Mendel’s laws in the early 1900s. The theoretical underpinnings of population genetics are discussed briefly in Chapter 3, and this chapter extends that discussion to include the use of phylogenomic high-throughput data such as microsatellites, RadTags, single-nucleotide polymorphisms (SNPs) and other genome reduction techniques. The nature of DNA variation at the population level has become extremely important in human genomics, and recent work has expanded our knowledge of how variable we are as a species. More importantly, this variation can be used in studies of human disease and to scan whole genomes for disease-related genes by the genome-wide association study (GWAS) approach. Classic approaches to population genetics, such as F statistics, and more recent approaches, such as STRUCTURE and multivariate statistical analysis, have broadened the view that population geneticists have of the natural world. These approaches are at the foundation of how we understand natural populations in an evolutionary context.

High-Throughput Methods and Population Genetics

When protein electrophoresis was invented and used widely in the 1960’s, a group of individuals from a study population could be examine...