Evolutionary developmental biology in the context of Graham Budd

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.

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.

Ontogeny (also ontogenesis) is the origination and development of an organism (both physical and psychological, e.g., moral development), usually from the time of fertilization of the egg to adult. The term can also be used to refer to the study of the entirety of an organism's lifespan.

Ontogeny is the developmental history of an organism within its own lifetime, as distinct from phylogeny, which refers to the evolutionary history of a species. Another way to think of ontogeny is that it is the process of an organism going through all of the developmental stages over its lifetime. The developmental history includes all the developmental events that occur during the existence of an organism, beginning with the changes in the egg at the time of fertilization and events from the time of birth or hatching and afterward (i.e., growth, remolding of body shape, development of secondary sexual characteristics, etc.). While developmental (i.e., ontogenetic) processes can influence subsequent evolutionary (e.g., phylogenetic) processes (see evolutionary developmental biology and recapitulation theory), individual organisms develop (ontogeny), while species evolve (phylogeny).

A body plan, Bauplan (pl. German: Baupläne), or ground plan is a set of morphological features common to many members of a phylum of animals. The vertebrates share one body plan, while invertebrates have many.

This term, usually applied to animals, envisages a "blueprint" encompassing aspects such as symmetry, layers, segmentation, nerve, limb, and gut disposition. Evolutionary developmental biology seeks to explain the origins of diverse body plans.

Hox genes, a subset of homeobox genes, are a group of related genes that specify regions of the body plan of an embryo along the head-tail axis of animals. Hox proteins encode and specify the characteristics of 'position', ensuring that the correct structures form in the correct places of the body. For example, Hox genes in insects specify which appendages form on a segment (for example, legs, antennae, and wings in fruit flies), and Hox genes in vertebrates specify the types and shape of vertebrae that will form. In segmented animals, Hox proteins thus confer segmental or positional identity, but do not form the actual segments themselves.

Studies on Hox genes in ciliated larvae have shown they are only expressed in future adult tissues. In larvae with gradual metamorphosis the Hox genes are activated in tissues of the larval body, generally in the trunk region, that will be maintained through metamorphosis. In larvae with complete metamorphosis the Hox genes are mainly expressed in juvenile rudiments and are absent in the transient larval tissues. The larvae of the hemichordate species Schizocardium californicum and the pilidium larva of Nemertea do not express Hox genes.

Sir Richard Owen KCB FRS FRMS (20 July 1804 – 18 December 1892) was an English biologist, comparative anatomist and palaeontologist. Owen is generally considered to have been an outstanding naturalist with a remarkable gift for interpreting fossils.

Owen produced a vast array of scientific work, but is probably best remembered today for coining the word Dinosauria (meaning "Terrible Reptile" or "Fearfully Great Reptile"). An outspoken critic of Charles Darwin's theory of evolution by natural selection, Owen agreed with Darwin that evolution occurred but thought it was more complex than outlined in Darwin's On the Origin of Species. Owen's approach to evolution can be considered to have anticipated the issues that have gained greater attention with the recent emergence of evolutionary developmental biology.

Étienne Geoffroy Saint-Hilaire (French pronunciation: [etjɛn ʒɔfʁwa sɛ̃t‿ilɛʁ]; 15 April 1772 – 19 June 1844) was a French naturalist who established the principle of "unity of composition". He was a colleague of Jean-Baptiste Lamarck and expanded and defended Lamarck's evolutionary theories. Geoffroy's scientific views had a transcendental flavor (unlike Lamarck's materialistic views) and were similar to those of German morphologists like Lorenz Oken. He believed in the underlying unity of organismal design, and the possibility of the transmutation of species in time, amassing evidence for his claims through research in comparative anatomy, paleontology, and embryology. He is considered as a predecessor of the evo-devo evolutionary concept.

In molecular biology and genetics, transcriptional regulation is the means by which a cell regulates the conversion of DNA to RNA (transcription), thereby orchestrating gene activity. A single gene can be regulated in a range of ways, from altering the number of copies of RNA that are transcribed, to the temporal control of when the gene is transcribed. This control allows the cell or organism to respond to a variety of intra- and extracellular signals and thus mount a response. Some examples of this include producing the mRNA that encode enzymes to adapt to a change in a food source, producing the gene products involved in cell cycle specific activities, and producing the gene products responsible for cellular differentiation in multicellular eukaryotes, as studied in evolutionary developmental biology.

The regulation of transcription is a vital process in all living organisms. It is orchestrated by transcription factors and other proteins working in concert to finely tune the amount of RNA being produced through a variety of mechanisms. Bacteria and eukaryotes have very different strategies of accomplishing control over transcription, but some important features remain conserved between the two. Most importantly is the idea of combinatorial control, which is that any given gene is likely controlled by a specific combination of factors to control transcription. In a hypothetical example, the factors A and B might regulate a distinct set of genes from the combination of factors A and C. This combinatorial nature extends to complexes of far more than two proteins, and allows a very small subset (less than 10%) of the genome to control the transcriptional program of the entire cell.

A gene (or genetic) regulatory network (GRN) is a collection of molecular regulators that interact with each other and with other substances in the cell to govern the gene expression levels of mRNA and proteins which, in turn, determine the function of the cell. GRN also play a central role in morphogenesis, the creation of body structures, which in turn is central to evolutionary developmental biology (evo-devo).

The regulator can be DNA, RNA, protein or any combination of two or more of these three that form a complex, such as a specific sequence of DNA and a transcription factor to activate that sequence. The interaction can be direct or indirect (through transcribed RNA or translated protein). In general, each mRNA molecule goes on to make a specific protein (or set of proteins). In some cases this protein will be structural, and will accumulate at the cell membrane or within the cell to give it particular structural properties. In other cases the protein will be an enzyme, i.e., a micro-machine that catalyses a certain reaction, such as the breakdown of a food source or toxin. Some proteins though serve only to activate other genes, and these are the transcription factors that are the main players in regulatory networks or cascades. By binding to the promoter region at the start of other genes they turn them on, initiating the production of another protein, and so on. Some transcription factors are inhibitory.

The theory of recapitulation, also called the biogenetic law or embryological parallelism—often expressed using Ernst Haeckel's phrase "ontogeny recapitulates phylogeny"—is a historical hypothesis that the development of the embryo of an animal, from fertilization to gestation or hatching (ontogeny), goes through stages resembling or representing successive adult stages in the evolution of the animal's remote ancestors (phylogeny). It was formulated in the 1820s by Étienne Serres based on the work of Johann Friedrich Meckel, after whom it is also known as the Meckel–Serres law.

Since embryos also evolve in different ways, the shortcomings of the theory had been recognized by the early 20th century, and it had been relegated to "biological mythology" by the mid-20th century. New discoveries in evolutionary developmental biology (Evo Devo) are providing explanations for these phenomena on a molecular level.

Conrad Hal Waddington CBE FRS FRSE (8 November 1905 – 26 September 1975) was a British developmental biologist, paleontologist, geneticist, embryologist and philosopher who laid the foundations for systems biology, epigenetics, and evolutionary developmental biology.

His theory of genetic assimilation probably has a Darwinian explanation, which contrast with the fact that Waddington himself was very critic about the notion of natural selection and Neo-Darwinism. Leading evolutionary biologists including Theodosius Dobzhansky and Ernst Mayr considered that Waddington was using genetic assimilation to support so-called Lamarckian inheritance, the acquisition of inherited characteristics through the effects of the environment during an organism's lifetime.

Neoteny (/niˈɒtəni/), also called juvenilization, is the delaying or slowing of the physiological, or somatic, development of an organism, typically an animal. Neoteny in modern humans is more significant than in other primates. In progenesis or paedogenesis, sexual development is accelerated.

Both neoteny and progenesis result in paedomorphism (as having the form typical of children) or paedomorphosis (changing towards forms typical of children), a type of heterochrony. It is the retention in adults of traits previously seen only in the young. Such retention is important in evolutionary biology, domestication, and evolutionary developmental biology. Some authors define paedomorphism as the retention of larval traits, as seen in salamanders.

The order Chiroptera, comprising all bats, has evolved the unique mammalian adaptation of flight. Bat wings are modified tetrapod forelimbs. Because bats are mammals, the skeletal structures in their wings are morphologically homologous to the skeletal components found in other tetrapod forelimbs. Through adaptive evolution these structures in bats have undergone many morphological changes, such as webbed digits, elongation of the forelimb, and reduction in bone thickness. Recently, there have been comparative studies of mouse and bat forelimb development to understand the genetic basis of morphological evolution. Consequently, the bat wing is a valuable evo-devo model for studying the evolution of vertebrate limb diversity.

Cis-regulatory elements (CREs) or cis-regulatory modules (CRMs) are regions of non-coding DNA which regulate the transcription of neighboring genes. CREs are vital components of genetic regulatory networks, which in turn control morphogenesis, the development of anatomy, and other aspects of embryonic development, studied in evolutionary developmental biology.

CREs are found in the vicinity of the genes that they regulate. CREs typically regulate gene transcription by binding to transcription factors. A single transcription factor may bind to many CREs, and hence control the expression of many genes (pleiotropy). The Latin prefix cis means "on this side", i.e. on the same molecule of DNA as the gene(s) to be transcribed.

In evolutionary developmental biology, homeosis is the transformation of one organ into another, arising from mutation in or misexpression of certain developmentally critical genes, specifically homeotic genes. In animals, these developmental genes specifically control the development of organs on their anteroposterior axis. In plants, however, the developmental genes affected by homeosis may control anything from the development of a stamen or petals to the development of chlorophyll. Homeosis may be caused by mutations in Hox genes, found in animals, or others such as the MADS-box family in plants. Homeosis is a characteristic that has helped insects become as successful and diverse as they are.

Homeotic mutations work by changing segment identity during development. For example, the Ultrabithorax genotype gives a phenotype wherein metathoracic and first abdominal segments become mesothoracic segments. Another well-known example is Antennapedia: a gain-of-function allele causes legs to develop in the place of antennae.