In evolutionary developmental biology, the concept of deep homology is used to describe cases where growth and differentiation processes are governed by genetic mechanisms that are homologous and deeply conserved across a wide range of species.
In evolutionary developmental biology, the concept of deep homology is used to describe cases where growth and differentiation processes are governed by genetic mechanisms that are homologous and deeply conserved across a wide range of species.
In 1822, the French zoologist Étienne Geoffroy Saint-Hilaire dissected a crayfish, discovering that its body is organised like a vertebrate's, but inverted belly to back (dorsoventrally): [1]
I just found that all the soft organs, that is to say, the principal organs of life are found in crustaceans, and so in insects, in the same order, in the same relationships and with the same arrangement as their analogues in the high vertebrate animals ... What was my surprise, and I may add, my admiration, seeing [such] a rule ... [1]
Geoffroy's homology theory was denounced by the leading French zoologist of his day, Georges Cuvier, but in 1994, Geoffroy was shown to be correct. [1] In 1915, Santiago Ramon y Cajal mapped the neural connections of the optic lobes of a fly, finding that these resembled those of vertebrates. [1] In 1978, Edward B. Lewis helped to found evolutionary developmental biology, discovering that homeotic genes regulated embryonic development in fruit flies. [1]
In 1997, the term deep homology first appeared in a paper by Neil Shubin, Cliff Tabin, and Sean B. Carroll, describing the apparent relatedness in genetic regulatory apparatuses which indicated evolutionary similarities in disparate animal features. [2]
Whereas ordinary homology is seen in the pattern of structures such as limb bones of mammals that are evidently related, deep homology can apply to groups of animals that have quite dissimilar anatomy: vertebrates (with endoskeletons made of bone and cartilage) and arthropods (with exoskeletons made of chitin) nevertheless have limbs that are constructed using similar recipes or "algorithms". [2] [3] [4] [5]
Within the metazoa, homeotic genes control differentiation along major body axes, and pax genes (especially PAX6) help to control the development of the eye and other sensory organs. The deep homology applies across widely separated groups, such as in the eyes of mammals and the structurally quite different compound eyes of insects. [3]
Similarly, hox genes help to form an animal's segmentation pattern. HoxA and HoxD, that regulate finger and toe formation in mice, control the development of ray fins in zebrafish; these structures had until then been considered non-homologous. [6]
There is a possible deep homology among animals that use acoustic communication, such as songbirds and humans, which may share unmutated versions of the FOXP2 gene. [7]
In modern day biology, the depth of understanding deep homology has evolved into focusing on the molecular and genetic mechanisms and functions rather than simple morphology. Cancer stem cells (CSCs) are a population of cells within a tumor that have the ability to self-renew and differentiate into different cell types, similar to normal stem cells. The stem cell theory of cancer suggests that there is a subpopulation of cells, referred to as cancer stem cells, that have certain characteristics that make them unique among other types of cells within a cancer. The traits that are included in CSCs are that they multiply indefinitely, are resistant to chemotherapy, and are proposed to be responsible for relapse after therapy. [8]
The unicellular life cycle of cancer and Entamoeba is uniquely similar, and thus contradicts the molecular phylostratigraphic theory for the origin of cancer. This deep relationship between the two cell systems is supported by the "amoeba model", which provides a greater understanding of the biology of cancer from the evolutionary perspective. [9] The G + S life cycle of Entamoeba is the closest common ancestor than compared to any other life cycle of unicellular organisms. Similarly, both cell systems, amoeba and cancer, use the deep homologous G + S gene module that was evolved by a common ancestor. Some parallels that they share are too close for coincidence:
(i) A reproductive asexual germ-line capable of forming germ-line stem cells (GSCs, referred to as CSCs in cancer) and a somatic cell line without reproductive GSC function; (ii) Germ and soma cells that proliferate through asymmetric and symmetric cell cycles and can interconvert by transitioning from germ to soma (GST) and from soma to germ (SGT); both processes are referred to as MET and EMT in cancer; (iii) Oxygen-sensitive germlines that irreversibly lose their reproductive function due to irreparable DNA damage caused by excess oxygen; (iv) DNA damage repair (DDR) mechanisms to repair DNA replication and polyploidization defects and maintain genomic integrity of nascent GSCs/CSCs; (v) DNA DSB repair mechanisms via MGRS and PGCC structures, with or without homologous cell fusion. [9]
MGRSs are also known in medical terms as “pre-existing Polypoid Giant Cancer Cells (PGCCs)” and are frequently observed in untreated cancers.[ citation needed ] In cancer, the reproductive germ-line cycle starts with a precursor cell. This cell will then polyploidize within a cell envelope. This cancer germ-line undergoes a process of development that is similar to the Entamoeba germline. A significant trace of deep homology can be found in mammalian germ-line stem cells. Based on a previous hypothesis, the germ-line is the common ancestor in somatic stem cell lineages. Daughter GSCs are the only stem cells that have the capability of passing genetic information throughout generations. [9]
Overall, the application of deep homology to the study of CSCs has the potential to improve the understanding of the molecular and genetic mechanisms that drive cancer progression, and may lead to the development of new treatments that target CSCs specifically. It can also lead to a better implementation of existing anti-cancer therapies.
In 2010, a team led by Edward Marcotte developed an algorithm that identifies deeply homologous genetic modules in unicellular organisms, plants, and animals based on phenotypes (such as traits and developmental defects). The technique aligns phenotypes across organisms based on orthology (a type of homology) of genes involved in the phenotypes. [10] [11]
Biology – The natural science that studies life. Areas of focus include structure, function, growth, origin, evolution, distribution, and taxonomy.
Evolutionary developmental biology is a field of biological research that compares the developmental processes of different organisms to infer how developmental processes evolved.
A homeobox is a DNA sequence, around 180 base pairs long, that regulates large-scale anatomical features in the early stages of embryonic development. Mutations in a homeobox may change large-scale anatomical features of the full-grown organism.
Gene knockouts are a widely used genetic engineering technique that involves the targeted removal or inactivation of a specific gene within an organism's genome. This can be done through a variety of methods, including homologous recombination, CRISPR-Cas9, and TALENs.
In biology, homology is similarity due to shared ancestry between a pair of structures or genes in different taxa. A common example of homologous structures is the forelimbs of vertebrates, where the wings of bats and birds, the arms of primates, the front flippers of whales and the forelegs of four-legged vertebrates like dogs and crocodiles are all derived from the same ancestral tetrapod structure. Evolutionary biology explains homologous structures adapted to different purposes as the result of descent with modification from a common ancestor. The term was first applied to biology in a non-evolutionary context by the anatomist Richard Owen in 1843. Homology was later explained by Charles Darwin's theory of evolution in 1859, but had been observed before this, from Aristotle onwards, and it was explicitly analysed by Pierre Belon in 1555.
A germ cell is any cell that gives rise to the gametes of an organism that reproduces sexually. In many animals, the germ cells originate in the primitive streak and migrate via the gut of an embryo to the developing gonads. There, they undergo meiosis, followed by cellular differentiation into mature gametes, either eggs or sperm. Unlike animals, plants do not have germ cells designated in early development. Instead, germ cells can arise from somatic cells in the adult, such as the floral meristem of flowering plants.
Evolutionary biology is the subfield of biology that studies the evolutionary processes that produced the diversity of life on Earth. It is also defined as the study of the history of life forms on Earth. Evolution holds that all species are related and gradually change over generations. In a population, the genetic variations affect the phenotypes of an organism. These changes in the phenotypes will be an advantage to some organisms, which will then be passed onto their offspring. Some examples of evolution in species over many generations are the peppered moth and flightless birds. In the 1930s, 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.
This is a list of topics in evolutionary biology.
Sequence homology is the biological homology between DNA, RNA, or protein sequences, defined in terms of shared ancestry in the evolutionary history of life. Two segments of DNA can have shared ancestry because of three phenomena: either a speciation event (orthologs), or a duplication event (paralogs), or else a horizontal gene transfer event (xenologs).
Pharyngeal slits are filter-feeding organs found among deuterostomes. Pharyngeal slits are repeated openings that appear along the pharynx caudal to the mouth. With this position, they allow for the movement of water in the mouth and out the pharyngeal slits. It is postulated that this is how pharyngeal slits first assisted in filter-feeding, and later, with the addition of gills along their walls, aided in respiration of aquatic chordates. These repeated segments are controlled by similar developmental mechanisms. Some hemichordate species can have as many as 200 gill slits. Pharyngeal clefts resembling gill slits are transiently present during the embryonic stages of tetrapod development. The presence of pharyngeal arches and clefts in the neck of the developing human embryo famously led Ernst Haeckel to postulate that "ontogeny recapitulates phylogeny"; this hypothesis, while false, contains elements of truth, as explored by Stephen Jay Gould in Ontogeny and Phylogeny. However, it is now accepted that it is the vertebrate pharyngeal pouches and not the neck slits that are homologous to the pharyngeal slits of invertebrate chordates. Pharyngeal arches, pouches, and clefts are, at some stage of life, found in all chordates. One theory of their origin is the fusion of nephridia which opened both on the outside and the gut, creating openings between the gut and the environment.
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, 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.
A body plan, Bauplan, 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.
Biological or process structuralism is a school of biological thought that objects to an exclusively Darwinian or adaptationist explanation of natural selection such as is described in the 20th century's modern synthesis. It proposes instead that evolution is guided differently, basically by more or less physical forces which shape the development of an animal's body, and sometimes implies that these forces supersede selection altogether.
Phytomorphology is the study of the physical form and external structure of plants. This is usually considered distinct from plant anatomy, which is the study of the internal structure of plants, especially at the microscopic level. Plant morphology is useful in the visual identification of plants. Recent studies in molecular biology started to investigate the molecular processes involved in determining the conservation and diversification of plant morphologies. In these studies transcriptome conservation patterns were found to mark crucial ontogenetic transitions during the plant life cycle which may result in evolutionary constraints limiting diversification.
Stem-cell niche refers to a microenvironment, within the specific anatomic location where stem cells are found, which interacts with stem cells to regulate cell fate. The word 'niche' can be in reference to the in vivo or in vitro stem-cell microenvironment. During embryonic development, various niche factors act on embryonic stem cells to alter gene expression, and induce their proliferation or differentiation for the development of the fetus. Within the human body, stem-cell niches maintain adult stem cells in a quiescent state, but after tissue injury, the surrounding micro-environment actively signals to stem cells to promote either self-renewal or differentiation to form new tissues. Several factors are important to regulate stem-cell characteristics within the niche: cell–cell interactions between stem cells, as well as interactions between stem cells and neighbouring differentiated cells, interactions between stem cells and adhesion molecules, extracellular matrix components, the oxygen tension, growth factors, cytokines, and the physicochemical nature of the environment including the pH, ionic strength and metabolites, like ATP, are also important. The stem cells and niche may induce each other during development and reciprocally signal to maintain each other during adulthood.
Evolutionary developmental biology (evo-devo) is the study of developmental programs and patterns from an evolutionary perspective. It seeks to understand the various influences shaping the form and nature of life on the planet. Evo-devo arose as a separate branch of science rather recently. An early sign of this occurred in 1999.
The following outline is provided as an overview of and topical guide to genetics:
How the Snake Lost Its Legs: Curious Tales from the Frontier of Evo-Devo is a 2014 book on evolutionary developmental biology by Lewis I. Held, Jr. The title pays homage to Rudyard Kipling's Just So Stories, but the "tales" are strictly scientific, explaining how a wide range of animal features evolved, in molecular detail. The book has been admired by other biologists as both accurate and accessible.
Cassandra Extavour is a Canadian geneticist, researcher of organismic and evolutionary biology, professor of molecular and cell biology at Harvard University, and a classical singer. Her research has focused on evolutionary and developmental genetics. She is known for demonstrating that germ cells engage in cell to cell competition before becoming a gamete, which indicates that natural selection can affect and change genetic material before adult sex reproduction takes place. She was also the Director of EDEN, a National Science Foundation-funded research collaborative that encouraged scientists working on organisms other than the standard lab model organisms to share protocols and techniques.
Germ-Soma Differentiation is the process by which organisms develop distinct germline and somatic cells. The development of cell differentiation has been one of the critical aspects of the evolution of multicellularity and sexual reproduction in organisms. Multicellularity has evolved upwards of 25 times, and due to this there is great possibility that multiple factors have shaped the differentiation of cells. There are three general types of cells: germ cells, somatic cells, and stem cells. Germ cells lead to the production of gametes, while somatic cells perform all other functions within the body. Within the broad category of somatic cells, there is further specialization as cells become specified to certain tissues and functions. In addition, stem cell are undifferentiated cells which can develop into a specialized cell and are the earliest type of cell in a cell lineage. Due to the differentiation in function, somatic cells are found ony in multicellular organisms, as in unicellular ones the purposes of somatic and germ cells are consolidated in one cell.