C value: The amount of DNA comprising the haploid genome for a given species (picograms per cell; 2-3 pg in mammals). The C value paradox is the lack of correlation between the C values of species and their evolutionary complexity. For example, some amphibians have 30 times as much DNA as we have but not more complex than humans.
CAAT box: A highly conserved DNA sequence found about 75 bp 5' to the site of transcription in eukaryotic genes. Its specific (trans-acting) transcription factor is CTF-1 (NF-1) (see also TATA / Goldberg-Hogness box).
Caenorhabditis elegans: A normally self-fertilizing hermaphrodite soil nematode whose developmental genetics has been extensively studied. It is no more than 1 mm long. Loss of an X chromosome by meiotic disjunction leads to the production of males. The genetic basis of apoptosis was first shown in C.elegans in 1986. It has five equally sized chromosomes and it is the first animal whose whole genome has been sequenced (in 1998). The 97 Mbp genome contains 19,000 genes on 6 chromosomes. About 74% of human genes have their homologues in the C.elegans genome. Links to the C.elegans website and an introduction to C.elegans.
Calcareous: Composed of calcium or calcium carbonate.
Cambrian: Cambria is the old name for Wales (UK) where the first skeletalized animal fossils were found. The first period in the Palaeozoic era marked by the occurrence of many forms of invertebrate life (540-500 Mya). The sudden appearance of the major animal phyla in the fossil record during the Cambrian period is called Cambrian explosion.
Canal plate (x-plate): A narrow elongated plate found on the epitheca of some thecate dinokont species ventral to the APC.
Cap site: The initiation site of transcription in a eukaryotic gene. The initiation of translation of most eukaryotic mRNAs involves recognition of the cap followed by either the first downstream AUG or by a 5' proximal AUG with a consensus sequence surrounding it (like the bacterial Shine-Dalgarno or the viral Kozak sequence). Such a consensus sequence has not been recognized in eukaryotes yet.
Cap: A methylated guanine residue (GTP) which is added to the 5' end of eukaryotic mRNAs in a post-transcriptional reaction. It protects the mRNA against 5'- exonuclease.
carnivore flesh-eating organism
Carnivore: An animal that feeds on the flesh of other animals. (See PARASITISM and PREDATION.
Cartilaginous fish(Class Chondrichthyes): The most primitive 'jawed' vertebrates evolved about 400 Mya. Their skeleton is composed of entirely cartilage. The Class includes the sharks, rays and skates (subclass Elasmobranchii) and the ratfish (subclass Holocephali). The earliest taxon which has both MHC class I and class II genes. The next step in the evolutionary ladder is the bony fish.
Caspase: Cysteine-containing aspartic acid-specific proteases involved in the execution phase of apoptosis. Fas/Fas ligand system is one activator of caspase-dependent apoptotic cell death.
Catarrhini: One of the two divisions (suborder) of Primates containing the old world monkeys and apes (extinct and extant). The other division is Platyrrhini (new world monkeys).
Catch Curve: A graph of the logarithm of number of fish taken at successive ages or sizes.
Catch Per Unit Of Effort: The catch of fish, in numbers or in weight, taken by a defined unit of fishing effort. Also called: catch per effort, fishing success, availability .
Catchability: The fraction of a fish stock which is caught by a defined unit of the fishing effort. When the unit is small enough that it catches only a small part of the stock -- 0.01 or less -- it can be used as an instantaneous rate in computing population change. (For fractions taken of various portions of the stock, see "vulnerability.") Also called: catchability coefficient, *force of fishing mortality
Catenate: Cells connected in a series; cells in chain formation.
Centric fusion: Fusion of the long arms of two acrocentric chromosomes [13,14,15,21,22] into a single chromosome having lost the short arms at the same time. Most often occurs as 21/21, 13/14, and 14/21 translocations. Apart from being an important cause of uniparental disomy, it may cause trisomy 21 (Down's syndrome) in the offspring. Human chromosome 2 is a result of a centric fusion between two ancestral ape chromosomes (gorillas have 24 pairs of chromosomes).
Centromere: Constricted region where sister chromatids are attached in mitotic chromosomes. The centromere is generally flanked by repetitive DNA sequences and it is late to replicate. The centromere is an A-T region of about 130 bp. It binds several proteins with high affinity to form the kinetochore which is the anchor for the mitotic spindle.
Cephalon: In trilobites, the head shield bearing the eyes, antennae, and mouth. More info?
Cestode: A parasitic, ribbon-like worm having no intestinal canal; class Cestoda (e.g., tapeworms).
Cetacea: An Order of marine mammals. The suborder Odontocetti includes dolphins, killer whales and toothed whales. Many of the great whales (such as the blue whale) belong to a different suborder (baleen whales or Mysticetti).
Chaetae: Stiff bristles characteristic of annelids.
Chaetognaths: free-swimming, carnivorous, pelagic, wormlike, planktonic animals; arrow worms
Chaperone: Any cellular protein that binds to an unfolded or partially folded target protein to prevent misfolding, aggregation, and/or degradation of it. Chaperones also facilitate the target protein's proper folding, translocation and assembly within cells, preventing inappropriate interactions with other proteins.
Character: Heritable trait possessed by an organism; characters are usually described in terms of their states, for example: "hair present" vs. "hair absent," where "hair" is the character, and "present" and "absent" are its states.
Character displacement: Forced evolution of dissimilar characters in related species where their ranges overlap. Elsewhere, where they exist on their own, their similarities are maintained.
Character release: This is the opposite of character displacement. Two closely related species become more alike in regions where their ranges do not overlap than in regions where they do.
Chela: The claw of an arthropod.
Chelicera: The first pair of appendages of a chelicerate arthropod. Originally a short clawed appendage, the chelicerae of many arachnids are highly modified for feeding; in spiders, for instance, they are modified into poisonous fangs.
Chemosynthesis: formation of organic compounds with energy derived from inorganic substances such as ammonia, sulfur and hydrogen
Chemotaxis: A response movement by an animal either toward or away from a specific chemical stimulus.
Chiasma (plural chiasmata): The points of physical overlap of nonsister chromatids crossing-over in meiosis.
Chi-like Sequence: An octamer nucleotide sequence (A/G - C/T - A/T - A/G - G - A/T - G - G) that creates a recombinational hotspot in the genome (originally discovered in coliphage lambda). MHC class I transmembrane domain length variation, frequent gene conversions and deletions in the MHC-linked 21-hydroxylase gene (CYP21), gene conversions within the MHC class II genes in mice and humans, many oncogene translocations (BCL2 for example) are attributed to chi-like sequences at the breakpoint region. It acts like a restriction site for recombinase.
Chlamydomonas: The unicellular green alga that is probably the closest living organism to the ancestor of green plants. It reproduces both asexually and sexually (two mating types). When reproduces sexually, the mitochondria are inherited from the (-) mating type and chloroplasts from the (+) mating type.
Chloramphenicol acetyl transferase (CAT): The bacterial gene for chloramphenicol, CAT, is commonly used as a reporter gene for investigating physiological gene regulation. Beta-galactosidase and luciferase genes can also be used for the same purpose.
Chlorophyll: Plant pigments found in chloroplasts which function as photoreceptors of light energy for photosynthesis.
Chloroplast: Membrane-bound organelle found in the cytoplasm of various eukaryotic organisms that contain the chlorophyll pigments and the enzyme systems for photosynthesis. Prokaryotic photosynthetic organisms do not have chloroplasts.
Chordata: A major phylum in the Kingdom Animalia. A chordate is characterized by the presence of a dorsal notochord at some stage of development and a dorsal hollow nerve chord. The phylum includes the subphyla Vertebrata, Cephalochordata, and Urochordata.
Chromatid: One of two copies of a replicated chromosome during mitosis. Together they are called sister chromatids. Each one becomes a daughter chromosome at anaphase of mitosis and at the second meiotic division.
Chromatin: The complex of DNA and associated histone and non-histone proteins that represents the normal state of genes in the nucleus. It exists in two forms: euchromatin can be transcribed, and heterochromatin is highly condensed and cannot be transcribed.
Chromista: A major taxon in the Kingdom Protoctista (also called Heterokonta). They are mostly photosynthetic algae but distinct from the rest of the algae. They have genetic material derived from four different ancestors (purple bacteria, cyanobacteria, red alga and green alga). Link to Chromista.
Chromosome:A tightly wound bundle of DNA and proteins found in the nucleus of eukaryotic cells. The number of chromosomes found in the haploid stage of an organism is represented as 1N. In the diploid stage of the organism there are two of each chromosome, one from the maternal genome and one from the paternal genome. The total number of chromosomes in the nucleus at this stage of the organism's life cycle is represented as 2N.
Ciguatera: A human intoxication caused by ingestion of tropical piscivorous reef fishes contaminated with toxin- producing benthic/epiphytic dinoflagellates. These fish accumulate biotoxins through the food chain (Steidinger 1993). More than 175 separate gastrointestinal, neurotoxic, or cardiovascular symptoms may be associated with this poisoning (Becker & Sanders 1991). In extreme cases death can result from respiratory failure. Although incidence is high, human mortality is low (Hallegraeff 1995).
Ciliates: This group of protists are most like animals in their behavior and complexity. The Paramecium is the representative of the Ciliates.
Cingular plates: In thecate dinokont species, the plates that make up the cingulum (designated with a 'c').
Cingulum: In dinokont species, this structure is usually a furrow (girdle) encircling the cell once or several times, and it can be displaced. In thecated species, the cingulum is made up of plates. This structure is missing in some desmokont- type cells (e.g. Prorocentrum).
Cis-acting gene: A gene acting on or co-operating with another gene on the same chromosome (see trans-acting gene).
Cistron: A DNA segment coding for a specific polypeptide, and includes its own start and stop codons. When an mRNA encodes two or more proteins, it is called polycistronic.
Clade: A monophyletic taxon; a group of organisms which includes the most recent common ancestor of all of its members and all of the descendants of that most recent common ancestor. From the Greek word "klados", meaning branch or twig.
Cladogenesis: The development of a new clade; the splitting of a single lineage into two distinct lineages; speciation.
Cladogram: A diagram, resulting from a cladistic analysis, which depicts a hypothetical branching sequence of lineages leading to the taxa under consideration. The points of branching within a cladogram are called nodes. All taxa occur at the endpoints of the cladogram.
Class switching: The process by which a IgM or IgD producing B lymphocyte switches to produce one of the secondary immunoglobulins (IgG, IgA or IgE) with the same antigen binding specificity.
Class: A category of classification (taxon); a subdivision of subphylum. The classes in the Subphylum Vertebrata are: Pisces (Fishes), Amphibia, Reptilia, Avis (Birds) and Mammalia.
Cline: A series of differing physical characteristics within a species or population, reflecting gradients or changes in the environment (e.g., body size or color).
Clitellum: In annelids, a swelling of the body towards the head of the animal, where the gonads are located. Both oligochaetes and leeches have a clitellum.
Closing plate (cp): A small plate located in the apical pore complex (APC) of some marine, armoured dinokont species, and associated with the apical pore (ap).
Cnidaria: See Coelamata.
Cnidocyst: The "stinging cell" of a cnidarian.
Coadaptation: Interaction of genes at the genotypic level. Natural selection acts on the complex product of such interactions rather than on individual locus. The correlated variation and adaptation present in two mutually dependent organisms.
Coalescence theory: The evolutionary theory that estimates the time for divergence from the last common ancestor. A lecture on Coalescent Theory.
Coalescence: Growing into each other, uniting into one whole.
Codominance: Equal effect on the phenotype of two alleles of the same locus (as opposed to recessive and dominant).
Codon bias: Although several codons code for a single amino acid, an organism may have a preferred codon for each amino acid. This is called codon bias.
Coefficient of relatedness: r = n(0.5)L where n is the alternative routes between the related individuals along which a particular allele can be inherited; L is the number of meiosis or generation links.
Coelacanth: Any member of a zoological family of largely extinct lobe-finned f: Any member of a zoological family of largely extinct lobe-finned fish (like the living genus Latimeria).
Coelom: Fluid-filled cavity within the body of an animal; usually refers to a cavity lined with specialized tissue peritoneum in which the gut is suspended. The structure and development of the coelom is an important character for recognizing major groups of animals.
Coelomata (Cnidaria): A phylum in the Animal Kingdom. They are invertebrate aquatic animals showing radial or biradial symmetry. Examples are corals, sea anemones, jelly fish. Co-evolution: Joint evolution of two unrelated species that have a close ecological relationship resulting in reciprocal adaptations as happens between host and parasite, and plant and insect.
Cognate molecule: A relative descended from a common ancestor. Usually used to describe the corresponding partner in a receptor-ligand complex.
Cohesive end: Also known as sticky end. Overhanging ends of a double-stranded DNA molecule that are capable of hybridizing with complementary ends.
Colonial organism: Organism consisting of semi-independent parts that do not exist as separate units; groups of organisms with specialized functions that form a coordinated unit
Colony: A group of organisms living in close proximity. An invertebrate colony is a close association of individuals of a species which are often mutually dependent and in physical contact with each other. A vertebrate colony is usually a group of individuals brought together for breeding and rearing young.
Commensalisms: an intimate association between different organisms in which one is benefited and the other is neither harmed nor benefited
Community: A naturally occurring group of plants and animals that live within a certain environment and interact with each other. Communities are often defined by a dominant species (e.g. kelp forest community) or the major physical characteristics of the area (e.g. mud flats).
Compensation depth: depth at which there is a balance between the oxygen produced by algae through photosynthesis and that consumed by them through respiration; net oxygen production is zero
Competition: Two types exist - interspecific and intraspecific. Interspecific completion exists when two or more species use one or more limited resources such as food, attachment sites protective cover, or dissolved ions. Intraspecific competition exist when individuals of a single species compete for limited resource needed for survival and reproduction. This form of competition includes the same resources involved in interspecific competition as well as mates and territories. It is generally more intense than interspecific competition because resource needs are essentially identical among conspecific. See NICHE.
Complementary (copy) DNA (cDNA): Single-stranded DNA produced from an RNA template (usually mRNA) by reverse transcriptase in vitro. It lacks the introns present in corresponding genomic DNA. It is most commonly made to use in PCR to amplify RNA (RT-PCR).
Compound eye: Found in many but not all arthropods, a compound eye is composed of a large number of small, closely packed simple eyes (ommatidia), each with its own lens and nerve receptors.
Compound heterozygote: An individual who is affected with an autosomal recessive disorder having two different mutations in homologous alleles.
Concave: Hollowed or rounded inward resembling the inside of a bowl.
Conditional Fishing Mortality Rate: The fraction of an initial stock which would be caught during the year (or season) if no other causes of mortality operated. (Also called fishing mortality rate).
Conditional Natural Mortality Rate: The fraction of an initial stock that would die from causes other than fishing during a year (or season), if there were no fishing mortality. Also called: annual natural mortality rate, seasonal natural mortality rate.
Congener: Referring to members of the same genus.
Congenic: Animals which have been bred to be genetically identical except for a single gene locus. This is achieved by superimposing the locus of interest on the genetic background of another by first crossing two inbred lines followed by extensive (about 20 generations) backcrossing hybrids to one parental line (the background strain) while selecting for the alleles of the locus of interest of the other. The result is an inbred strain uniquely identified by a difference at a single locus.
Conifers: Cone bearing trees. A Class of the Gymnospermae which includes needle-leaved trees such as pines and cypresses. Their flowers are in cones, and male and flower cones are separate. The oldest (britlecone pine) and the largest (sequoia) extant organisms belong to this Class. Their unique feature is the inheritance of cytoplasmic DNA (chloroplasts) via pollens.
Conjugation: In unicellular organisms, temporary cell contact between complementary genders and exchange of genetic material, as in the ciliate Paramecium aurelia, or one-way transfer of genes as in bacteria (see F Factor) and green alga Spirogyra.
Consanguineous matings: Matings between two individuals who share a common ancestor in the preceding two or three generations.
Consensus sequence: The nucleotides or amino acids most commonly found at each positions of the sequences of related molecules.
Conservation Biology: A field of science that deals with threats to biodiversity. The goals of conservation biology are to investigate human impacts of biodiversity and to develop approaches to prevent extinction through stewardship of entire biological communities.
Consumer: animal that feeds on plants (primary consumer) or on other animals (secondary consumer)
Continental shelf: The submerged continental land mass, not usually deeper than 200 m. The shelf may extend from a few miles off the coastline to several hundred miles.
Continental slope: The steeply sloping seabed that connects the continental shelf and continental rise.
Convergence: Similarities which have arisen independently in two or more organisms that are not closely related. Contrast with homology.
Convergent evolution: Evolution of two or more different lineages towards similar morphology due to similar adaptive pressures. Examples of convergence are: fins or fin- like structures in fish, cuttlefish and whales; extreme similarity in alarm calls by five small birds; endothermy in dogs and ducks, wings of butterflies and birds.
Convex: Curved or rounded resembling the exterior of a sphere or circle.
Cope’s Rule: Animals tend to get larger during the course of their phyletic evolution.
Copepoda: A subclass of crustaceans with about 4,500 species, including several specialized parasitic orders. The free-living species are small (one to several mm.) and have cylindrical bodies, one median eye, and two long antennae. One order is planktonic (Calanoida), one is benthic (Harpacticoida), and one has both planktonic and benthic species (Cyclopoida). In most species, the head appendages form a complex apparatus used to sweep in and possibly filter prey (especially algae). Thoracic appendages are used for swimming or crawling on the bottom. One of the most abundant group of animals on earth, they are a major link in aquatic food webs.
Cope's 'law of the unspecialized': The evolutionary novelties associated with new major taxa are more likely to originate from a generalized member of an ancestral taxon rather than a specialized member.
Coral: colonial animal that secretes a hard outer calcareous skeleton; the skeletons of coral animals form in part the framework for warm-water reefs
Costae: A rib or rib-like structure, often located in the apical pore complex of thecated species; e.g. Coolia monotis.
Coupling (cis-arrangement): The condition in which a double heterozygote has received two linked mutations from one parent and their wild-type alleles from the other parent, e.g., a b / + + (as opposed to a + / + b; see also repulsion).
CpG island: Repetitive CpG doublets creating a region of DNA greater than 200 bp in length with a G+C content of more than 0.5 and an observed/expected presence of CpG more than 0.6. Usually associated with transcription-initiation regions of (housekeeping) genes transcribed at low rates that do not contain a TATA box. The CpG-rich stretch of 20-50 nucleotides occurs within the first 100-200 bases upstream of the start site region (where promoter-proximal elements reside). A trans-acting transcription factor called SP1 recognizes the CpG islands (see also Htf islands). In vertebrates, many of the nontranscribed genes (and the genes on the inactivated X chromosome) have a 5-methyl group on the C residue in CpG dinucleotides in transcription-control regions. On the other hand, many genes with restricted expression patterns have (methylated) CpG islands located downstream of transcription initiation does not block elongation of the transcript (see also Methylation paradox).
Crepuscular: Relates to animals whose peak activity is during the twilight hours of dawn and dusk.
Cretaceous: The youngest of the three geologic periods of the Mesozoic era (145 to 65 Mya).
Critical Size: The average size of the fish in a year class at the time when the instantaneous rate of natural mortality equals the instantaneous rate of growth in weight for the year-class as a whole. Also called: *optimum size.
Crossing-over (recombination): The exchange of genetic material between non-sister chromatids of homologous chromosomes (i.e., between maternal and paternal chromosomes) during meiosis. This results in a new and unique combination of genes on the daughter chromosome which will be passed on to the offspring (if that particular gamete is involved in fertilization).
Crown group: All the taxa descended from a major cladogenesis event, recognized by possessing the clade's synapomorphy. See: stem group.
Crustacea: A large class of over 26,000 species of mostly aquatic arthropods having five pairs of head appendages, including laterally opposed jaw-like mandibles and two pairs of antennae.
Cryptic Colouration: To protect themselves against predators, many animals acquire colouring and markings to match and conceal them in their usual surroundings. For example the nudibranch (sea slug), Rostanga pulchra, is practically indiscernible from the red sponges on which it lays its eggs.
Cryptic female choice: Besides precopulatory female sexual selection, there are also postcopulatory selection processes going on in the female reproductive system. This less appreciated mechanism is the basis for differential fertilization which includes sperm selection as opposed to pollen selection in plants. This should not be confused with sperm competition / pollen tube competition (link to a book by Tim Birkhead on Sperm Selection).
Ctenophora: A phylum of mostly marine animals that have oval, jellylike bodies bearing eight rows of comb-like plates that aid swimming (e.g., ctenophores and comb jellies).
ctenophores transparent, planktonic animals, spherical or cylindrical in shape with rows of cilia; comb jellies
Cuticle: In animals, a multilayered, extracellular, external body covering, usually composed of fibrous molecules such as chitin or collagen, and sometimes strengthened by the deposition of minerals such as calcium carbonate.
Cyanobacteria: Unicellular, photosynthetic (photo-autotroph) prokaryote (in the Kingdom Monera). Formerly known as blue-green algae. It contains chlorophyll a but not chloroplast. They reproduce by fission and never sexually.
Cyst: Any dormant or resting nonmotile cell possessing a distinct cell wall.
Cytoplasm: Protoplasm within a plant or animal cell external to the nucleur membrane.