Common descent is a concept in evolutionary biology applicable when one species is the ancestor of two or more species later in time. According to modern evolutionary biology, all living beings could be descendants of a unique ancestor commonly referred to as the last universal common ancestor (LUCA) of all life on Earth.
In the fields of molecular biology and genetics, a genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA. The nuclear genome includes protein-coding genes and non-coding genes, other functional regions of the genome such as regulatory sequences, and often a substantial fraction of junk DNA with no evident function. Almost all eukaryotes have mitochondria and a small mitochondrial genome. Algae and plants also contain chloroplasts with a chloroplast genome.
Carl Richard Woese was an American microbiologist and biophysicist. Woese is famous for defining the Archaea in 1977 through a pioneering phylogenetic taxonomy of 16S ribosomal RNA, a technique that has revolutionized microbiology. He also originated the RNA world hypothesis in 1967, although not by that name. Woese held the Stanley O. Ikenberry Chair and was professor of microbiology at the University of Illinois Urbana–Champaign.
Non-coding DNA (ncDNA) sequences are components of an organism's DNA that do not encode protein sequences. Some non-coding DNA is transcribed into functional non-coding RNA molecules. Other functional regions of the non-coding DNA fraction include regulatory sequences that control gene expression; scaffold attachment regions; origins of DNA replication; centromeres; and telomeres. Some non-coding regions appear to be mostly nonfunctional, such as introns, pseudogenes, intergenic DNA, and fragments of transposons and viruses. Regions that are completely nonfunctional are called junk DNA.
Junk DNA is a DNA sequence that has no known biological function. Most organisms have some junk DNA in their genomes—mostly, pseudogenes and fragments of transposons and viruses—but it is possible that some organisms have substantial amounts of junk DNA.
Molecular evolution describes how inherited DNA and/or RNA change over evolutionary time, and the consequences of this for proteins and other components of cells and organisms. Molecular evolution is the basis of phylogenetic approaches to describing the tree of life. Molecular evolution overlaps with population genetics, especially on shorter timescales. Topics in molecular evolution include the origins of new genes, the genetic nature of complex traits, the genetic basis of adaptation and speciation, the evolution of development, and patterns and processes underlying genomic changes during evolution.
Comparative genomics is a branch of biological research that examines genome sequences across a spectrum of species, spanning from humans and mice to a diverse array of organisms from bacteria to chimpanzees. This large-scale holistic approach compares two or more genomes to discover the similarities and differences between the genomes and to study the biology of the individual genomes. Comparison of whole genome sequences provides a highly detailed view of how organisms are related to each other at the gene level. By comparing whole genome sequences, researchers gain insights into genetic relationships between organisms and study evolutionary changes. The major principle of comparative genomics is that common features of two organisms will often be encoded within the DNA that is evolutionarily conserved between them. Therefore, Comparative genomics provides a powerful tool for studying evolutionary changes among organisms, helping to identify genes that are conserved or common among species, as well as genes that give unique characteristics of each organism. Moreover, these studies can be performed at different levels of the genomes to obtain multiple perspectives about the organisms.
C-value is the amount, in picograms, of DNA contained within a haploid nucleus or one half the amount in a diploid somatic cell of a eukaryotic organism. In some cases, the terms C-value and genome size are used interchangeably; however, in polyploids the C-value may represent two or more genomes contained within the same nucleus. Greilhuber et al. have suggested some new layers of terminology and associated abbreviations to clarify this issue, but these somewhat complex additions are yet to be used by other authors.
Genome size is the total amount of DNA contained within one copy of a single complete genome. It is typically measured in terms of mass in picograms or less frequently in daltons, or as the total number of nucleotide base pairs, usually in megabases. One picogram is equal to 978 megabases. In diploid organisms, genome size is often used interchangeably with the term C-value.
Susumu Ohno was a Japanese-American geneticist and evolutionary biologist, and seminal researcher in the field of molecular evolution.
James Alan Shapiro is an American biologist, an expert in bacterial genetics and a professor in the Department of Biochemistry and Molecular Biology at the University of Chicago.
Evolutionary thought, the recognition that species change over time and the perceived understanding of how such processes work, has roots in antiquity—in the ideas of the ancient Greeks, Romans, Chinese, Church Fathers as well as in medieval Islamic science. With the beginnings of modern biological taxonomy in the late 17th century, two opposed ideas influenced Western biological thinking: essentialism, the belief that every species has essential characteristics that are unalterable, a concept which had developed from medieval Aristotelian metaphysics, and that fit well with natural theology; and the development of the new anti-Aristotelian approach to modern science: as the Enlightenment progressed, evolutionary cosmology and the mechanical philosophy spread from the physical sciences to natural history. Naturalists began to focus on the variability of species; the emergence of palaeontology with the concept of extinction further undermined static views of nature. In the early 19th century prior to Darwinism, Jean-Baptiste Lamarck (1744–1829) proposed his theory of the transmutation of species, the first fully formed theory of evolution.
George M. Weinstock is an American geneticist and microbiologist on the faculty of The Jackson Laboratory for Genomic Medicine, where he is a professor and the associate director for microbial genomics. Before joining The Jackson Laboratory, he taught at Washington University in St. Louis and served as associate director of The Genome Institute. Previously, Weinstock was co-director of the Human Genome Sequencing Center (HGSC) at Baylor College of Medicine in Houston, Texas, and Professor of Molecular and Human Genetics. He received his B.S. degree from the University of Michigan in 1970 and his Ph.D. from the Massachusetts Institute of Technology in 1977. He has spent most of his career taking genomic approaches to study fundamental biological processes.
Jonathan Andrew Eisen is an American evolutionary biologist, currently working at University of California, Davis. His academic research is in the fields of evolutionary biology, genomics and microbiology and he is the academic editor-in-chief of the open access journal PLOS Biology.
Microbial phylogenetics is the study of the manner in which various groups of microorganisms are genetically related. This helps to trace their evolution. To study these relationships biologists rely on comparative genomics, as physiology and comparative anatomy are not possible methods.
The following outline is provided as an overview of and topical guide to evolution:
Harris A. Lewin, an American biologist, is a professor of evolution and ecology and Robert and Rosabel Osborne Endowed Chair at the University of California, Davis. He is a member of the National Academy of Sciences. In 2011, Lewin won the Wolf Prize in Agriculture for his research into cattle genomics. Lewin chairs the working group for the Earth BioGenome Project, a moonshot for biology that aims to sequence, catalog, and characterize the genomes of all of Earth’s eukaryotic biodiversity over a period of 10 years. Lewin is a founding co-editor of the Annual Review of Animal Biosciences, first published in 2013.
The onion test is a way of assessing the validity of an argument for a functional role for junk DNA. It relates to the paradox that would emerge if the majority of eukaryotic non-coding DNA were assumed to be functional and the difficulty of reconciling that assumption with the diversity in genome sizes among species. The term "onion test" was originally proposed informally in a blog post by T. Ryan Gregory in order to help clarify the debate about junk DNA. The term has been mentioned in newspapers and online media, scientific journal articles, and a textbook. The test is defined as:
The onion test is a simple reality check for anyone who thinks they have come up with a universal function for junk DNA. Whatever your proposed function, ask yourself this question: Can I explain why an onion needs about five times more non-coding DNA for this function than a human?
Jose V. Lopez is an American-Filipino Molecular Biologist. He has been a faculty member and Professor of Biology at Nova Southeastern University (NSU) in Dania Beach, Florida, since 2007. Lopez has contributed as a co-founder of the Global Invertebrate Genomics Alliance (GIGA), a community of scientists. He has also participated in the "Porifera—Tree of Life," "Earth Microbiome," and Earth BioGenome projects.
