Molecular evolution in the context of Adaptation

Evolutionary biology is a subfield of biology that analyzes the four mechanisms of evolution: natural selection, mutation, genetic drift, and gene flow. The purpose of evolutionary biology is to observe the diversity of life on Earth. The idea of natural selection was first researched by Charles Darwin as he studied bird beaks. The discipline of evolutionary biology emerged through what Julian Huxley called the modern synthesis of understanding, from previously unrelated fields of biological research, such as genetics and ecology, systematics, and paleontology. Huxley was able to take what Charles Darwin discovered and elaborate to build on his understandings.

The investigational range of current research has widened to encompass the genetic architecture of adaptation, molecular evolution, and the different forces that contribute to evolution, such as sexual selection, genetic drift, and biogeography. The newer field of evolutionary developmental biology ("evo-devo") investigates how embryogenesis is controlled, thus yielding a wider synthesis that integrates developmental biology with the fields of study covered by the earlier evolutionary synthesis.

Species richness, or biodiversity, increases from the poles to the tropics for a wide variety of terrestrial and marine organisms, often referred to as the latitudinal diversity gradient. The latitudinal diversity gradient is one of the most widely recognized patterns in ecology. It has been observed to varying degrees in Earth's past. A parallel trend has been found with elevation (elevational diversity gradient), though this is less well-studied.

Explaining the latitudinal diversity gradient has been called one of the great contemporary challenges of biogeography and macroecology (Willig et al. 2003, Pimm and Brown 2004, Cardillo et al. 2005). The question "What determines patterns of species diversity?" was among the 25 key research themes for the future identified in 125th Anniversary issue of Science (July 2005). There is a lack of consensus among ecologists about the mechanisms underlying the pattern, and many hypotheses have been proposed and debated. A recent review noted that among the many conundrums associated with the latitudinal diversity gradient (or latitudinal biodiversity gradient) the causal relationship between rates of molecular evolution and speciation has yet to be demonstrated.

Molecular phylogenetics (/məˈlɛkjʊlər ˌfaɪloʊdʒəˈnɛtɪks, mɒ-, moʊ-/) is the branch of phylogeny that analyzes genetic, hereditary molecular differences, predominantly in DNA sequences, to gain information on an organism's evolutionary relationships. From these analyses, it is possible to determine the processes by which diversity among species has been achieved. The result of a molecular phylogenetic analysis is expressed in a phylogenetic tree. Molecular phylogenetics is one aspect of molecular systematics, a broader term that also includes the use of molecular data in taxonomy and biogeography.

Molecular phylogenetics and molecular evolution correlate. Molecular evolution is the process of selective changes (mutations) at a molecular level (genes, proteins, etc.) throughout various branches in the tree of life (evolution). Molecular phylogenetics makes inferences of the evolutionary relationships that arise due to molecular evolution and results in the construction of a phylogenetic tree.

Divergent evolution or divergent selection is the accumulation of differences between closely related populations within a species, sometimes leading to speciation. Divergent evolution is typically exhibited when two populations become separated by a geographic barrier (such as in allopatric or peripatric speciation) and experience different selective pressures that cause adaptations. After many generations and continual evolution, the populations become less able to interbreed with one another. The American naturalist J. T. Gulick (1832–1923) was the first to use the term "divergent evolution", with its use becoming widespread in modern evolutionary literature. Examples of divergence in nature are the adaptive radiation of the finches of the Galápagos, changes in mobbing behavior of the kittiwake, and the evolution of the modern-day dog from the wolf.

The term can also be applied in molecular evolution, such as to proteins that derive from homologous genes. Both orthologous genes (resulting from a speciation event) and paralogous genes (resulting from gene duplication) can illustrate divergent evolution. Through gene duplication, it is possible for divergent evolution to occur between two genes within a species. Similarities between species that have diverged are due to their common origin, so such similarities are homologies.

A living fossil is a term for an extant taxon that phenotypically resembles related species known only from the fossil record, though scientifically the term is deprecated and avoided. To be considered a living fossil, the fossil species must be old relative to the time of origin of the extant clade. Living fossils commonly are of species-poor lineages, but they need not be. While the body plan of a living fossil remains superficially similar, it is never the same species as the remote relatives it resembles, because genetic drift would inevitably change its chromosomal structure.

Living fossils exhibit stasis (also called "bradytely") over geologically long time scales. Popular literature may wrongly claim that a "living fossil" has undergone no significant evolution since fossil times, with practically no molecular evolution or morphological changes. Scientific investigations have repeatedly discredited such claims.

Evolutionary physiology is the study of the biological evolution of physiological structures and processes; that is, the manner in which the functional characteristics of organisms have responded to natural selection or sexual selection or changed by random genetic drift across multiple generations during the history of a population or species. It is a sub-discipline of both physiology and evolutionary biology. Practitioners in the field come from a variety of backgrounds, including physiology, evolutionary biology, ecology, and genetics.

Accordingly, the range of phenotypes studied by evolutionary physiologists is broad, including life history traits, behavior, whole-organism performance, functional morphology, biomechanics, anatomy, classical physiology, endocrinology, biochemistry, and molecular evolution. The field is closely related to comparative physiology, ecophysiology, and environmental physiology, and its findings are a major concern of evolutionary medicine. One definition that has been offered is "the study of the physiological basis of fitness, namely, correlated evolution (including constraints and trade-offs) of physiological form and function associated with the environment, diet, homeostasis, energy management, longevity, and mortality and life history characteristics".

Gene duplication (or chromosomal duplication or gene amplification) is a mechanism through which new genetic material is generated during molecular evolution. It can be defined as any duplication of a region of DNA that contains a gene. Gene duplications can arise as products of several types of errors in DNA replication and repair machinery as well as through fortuitous capture by selfish genetic elements. Common sources of gene duplications include ectopic recombination, retrotransposition event, aneuploidy, polyploidy, and replication slippage.

Émile Zuckerkandl (July 4, 1922 – November 9, 2013) was an Austrian-born French biologist considered one of the founders of the field of molecular evolution. He introduced, with Linus Pauling, the concept of the "molecular clock", which enabled the neutral theory of molecular evolution.

In molecular biology, a protein domain is a region of a protein's polypeptide chain that is self-stabilizing and that folds independently from the rest. Each domain forms a compact folded three-dimensional structure. Many proteins consist of several domains, and a domain may appear in a variety of different proteins. Molecular evolution uses domains as building blocks and these may be recombined in different arrangements to create proteins with different functions. In general, domains vary in length from between about 50 amino acids up to 250 amino acids in length. The shortest domains, such as zinc fingers, are stabilized by metal ions or disulfide bridges. Domains often form functional units, such as the calcium-binding EF hand domain of calmodulin. Because they are independently stable, domains can be "swapped" by genetic engineering between one protein and another to make chimeric proteins.

MEDLINE (Medical Literature Analysis and Retrieval System Online, or MEDLARS Online) is a bibliographic database of life sciences and biomedical information. It includes bibliographic information for articles from academic journals covering medicine, nursing, pharmacy, dentistry, veterinary medicine, and health care. MEDLINE also covers much of the literature in biology and biochemistry, as well as fields such as molecular evolution.

Compiled by the United States National Library of Medicine (NLM), MEDLINE is freely available on the Internet and searchable via PubMed and NLM's National Center for Biotechnology Information's Entrez system.

Richard Charles Lewontin (March 29, 1929 – July 4, 2021) was an American evolutionary biologist, mathematician, geneticist, and social commentator. A leader in developing the mathematical basis of population genetics and evolutionary theory, he applied techniques from molecular biology, such as gel electrophoresis, to questions of genetic variation and evolution. He was a self-described Marxist.

In a pair of seminal 1966 papers co-authored with J. L. Hubby in the journal Genetics, Lewontin helped set the stage for the modern field of molecular evolution. In 1979, he and Stephen Jay Gould introduced the term "spandrel" into evolutionary theory. From 1973 to 1998, he held an endowed chair in zoology and biology at Harvard University, and from 2003 until his death in 2021 he was a research professor there.

James Franklin Crow (January 18, 1916 – January 4, 2012) was Professor Emeritus of Genetics at the University of Wisconsin–Madison and a prominent population geneticist whose career spanned from the modern synthesis to the genomic era.

Some of his most significant peer-reviewed contributions were coauthored with Motoo Kimura, including those leading to the neutral theory of molecular evolution. He also wrote an influential introductory textbook on genetics and a more advanced one with Kimura. His graduate and undergraduate students and postdocs includes Alexey Kondrashov, James Bull, Joe Felsenstein, Russell Lande, Dan Hartl, and Wen-Hsiung Li.