VertebrateVertebrates (ˈvɜrtəbrɪts,_-ˌbreɪts) are animals with spinal cords and bony or cartilaginous backbones, including all mammals, birds, reptiles, amphibians and fish. The vertebrates consist of all the taxa within the subphylum Vertebrata (ˌvɜrtəˈbreɪtə) (chordates with backbones) and represent the overwhelming majority of the phylum Chordata, with currently about 69,963 species described.
Hox geneHox 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.
Topologically associating domainA topologically associating domain (TAD) is a self-interacting genomic region, meaning that DNA sequences within a TAD physically interact with each other more frequently than with sequences outside the TAD. The median size of a TAD in mouse cells is 880 kb, and they have similar sizes in non-mammalian species. Boundaries at both side of these domains are conserved between different mammalian cell types and even across species and are highly enriched with CCCTC-binding factor (CTCF) and cohesin.
Comparative genomicsComparative genomics is a field of biological research in which the genomic features of different organisms are compared. The genomic features may include the DNA sequence, genes, gene order, regulatory sequences, and other genomic structural landmarks. In this branch of genomics, whole or large parts of genomes resulting from genome projects are compared to study basic biological similarities and differences as well as evolutionary relationships between organisms.
Vertebrate paleontologyVertebrate paleontology is the subfield of paleontology that seeks to discover, through the study of fossilized remains, the behavior, reproduction and appearance of extinct animals with vertebrae or a notochord. It also tries to connect, by using the evolutionary timeline, the animals of the past and their modern-day relatives. The fossil record shows aspects of the meandering evolutionary path from early aquatic vertebrates to mammals, with a host of transitional fossils, though there are still large blank areas.
HomeoboxA 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. Homeoboxes are found within genes that are involved in the regulation of patterns of anatomical development (morphogenesis) in animals, fungi, plants, and numerous single cell eukaryotes.
GnathostomataGnathostomata (ˌnæθoʊ-'stɒmətə; from Greek: γνάθος (gnathos) "jaw" + στόμα (stoma) "mouth") are the jawed vertebrates. Gnathostome diversity comprises roughly 60,000 species, which accounts for 99% of all living vertebrates, including humans. In addition to opposing jaws, living gnathostomes have true teeth (a characteristic which has subsequently been lost in some), paired appendages (pectoral and pelvic fins, arms, legs, wings, etc.
ChromatinChromatin is a complex of DNA and protein found in eukaryotic cells. The primary function is to package long DNA molecules into more compact, denser structures. This prevents the strands from becoming tangled and also plays important roles in reinforcing the DNA during cell division, preventing DNA damage, and regulating gene expression and DNA replication. During mitosis and meiosis, chromatin facilitates proper segregation of the chromosomes in anaphase; the characteristic shapes of chromosomes visible during this stage are the result of DNA being coiled into highly condensed chromatin.
AgnathaAgnatha ('ægnəθə,_æg'neɪθə; ) is an infraphylum of jawless fish in the phylum Chordata, subphylum Vertebrata, consisting of both present (cyclostomes) and extinct (conodonts and ostracoderms) species. Among recent animals, cyclostomes are sister to all vertebrates with jaws, known as gnathostomes. Recent molecular data, both from rRNA and from mtDNA as well as embryological data, strongly supports the hypothesis that living agnathans, the cyclostomes, are monophyletic.
Gene regulatory networkA 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).
Topological defectTopological defects or solitons are irregularities or disruptions that occur within continuous fields or ordered states of matter. These defects, which can take various forms such as points, lines, or surfaces, are characterized by their stability and the fact that they cannot be 'smoothed out' or removed through continuous transformations of the field or material. They play a significant role in various areas of physics, including condensed matter physics, cosmology, and quantum field theory, and can have profound effects on the properties and behavior of the systems in which they occur.
Gene duplicationGene duplication (or chromosomal duplication or gene amplification) is a major 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.
Topological quantum numberIn physics, a topological quantum number (also called topological charge) is any quantity, in a physical theory, that takes on only one of a discrete set of values, due to topological considerations. Most commonly, topological quantum numbers are topological invariants associated with topological defects or soliton-type solutions of some set of differential equations modeling a physical system, as the solitons themselves owe their stability to topological considerations.
Cis-regulatory elementCis-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.
JawThe jaw is any opposable articulated structure at the entrance of the mouth, typically used for grasping and manipulating food. The term jaws is also broadly applied to the whole of the structures constituting the vault of the mouth and serving to open and close it and is part of the body plan of humans and most animals. In arthropods, the jaws are chitinous and oppose laterally, and may consist of mandibles or chelicerae. These jaws are often composed of numerous mouthparts.
Fish jawMost bony fishes have two sets of jaws made mainly of bone. The primary oral jaws open and close the mouth, and a second set of pharyngeal jaws are positioned at the back of the throat. The oral jaws are used to capture and manipulate prey by biting and crushing. The pharyngeal jaws, so-called because they are positioned within the pharynx, are used to further process the food and move it from the mouth to the stomach. Cartilaginous fishes, such as sharks and rays, have one set of oral jaws made mainly of cartilage.
Chromatin remodelingChromatin remodeling is the dynamic modification of chromatin architecture to allow access of condensed genomic DNA to the regulatory transcription machinery proteins, and thereby control gene expression. Such remodeling is principally carried out by 1) covalent histone modifications by specific enzymes, e.g., histone acetyltransferases (HATs), deacetylases, methyltransferases, and kinases, and 2) ATP-dependent chromatin remodeling complexes which either move, eject or restructure nucleosomes.
Transcriptional regulationIn 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.
PaleopolyploidyPaleopolyploidy is the result of genome duplications which occurred at least several million years ago (MYA). Such an event could either double the genome of a single species (autopolyploidy) or combine those of two species (allopolyploidy). Because of functional redundancy, genes are rapidly silenced or lost from the duplicated genomes. Most paleopolyploids, through evolutionary time, have lost their polyploid status through a process called diploidization, and are currently considered diploids, e.g.
PolyploidyPolyploidy is a condition in which the cells of an organism have more than one pair of (homologous) chromosomes. Most species whose cells have nuclei (eukaryotes) are diploid, meaning they have two complete sets of chromosomes, one from each of two parents; each set contains the same number of chromosomes, and the chromosomes are joined in pairs of homologous chromosomes. However, some organisms are polyploid. Polyploidy is especially common in plants. Most eukaryotes have diploid somatic cells, but produce haploid gametes (eggs and sperm) by meiosis.
