Tree of Life Glossary

The ToL Glossary is still under construction. We expect to greatly expand it over the next few months. The current page contains a listing of all the available ToL Glossary terms.

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aboral:

Relating to position: away from the mouth (cf. adoral).

abyssopelagic: (abyssopelagic zone)

The part of the ocean that extends from 4000m to the sea floor. This zone is characterized by near- freezing temperatures and crushing water pressure.

actinopod: (actinopods)

A type of pseudopod, needle-shaped, with internal skeleton formed from arrays of microtubules.

adoral:

Relating to position: toward the mouth (cf. aboral).

aerial:

Pertaining to the air - as opposed to the land (terrestrial) or the water (aquatic).

aestivation: (aestivate, estivate, estivation)

In animals: a state of dormancy/inactivity during the summer.

In plants: the arrangement of sepals and petals or their lobes in an unexpanded flower bud.

alga: (algal, algae)

A polyphyletic grouping of organisms with chloroplasts. Now divided into blue-green algae (eubacteria), cryptomonads, chlorarachniophytes, glaucophytes, dinoflagellates and other alveolates, euglenids (a group of Euglenozoa), various stramenopiles (also referred to as chromophytes, chrysophytes, heterokonts - including the diatoms and brown algae), haptophytes (= prasinophytes), green algae (green plants), and red algae. For more information see Algae: Protists with Chloroplasts.

allopatry: (allopatric)

Species or populations occupying separate geographic areas. Compare to sympatry.

aloricate:

No lorica present.

amino acid: (amino acids)

Molecule that serves as the basic structural unit of proteins. General formula: RCH(NH₂)COOH, with the side group (R) specific for each individual amino acid.

amoeba: (amoebae)

Any organism in a polyphyletic grouping of organisms which move and feed using pseudopodia. For more information about amoebae see Amoebae: Protists Which Move and Feed Using Pseudopodia.

amoeboid:

Like an amoeba. Usually means that the organism has the capacity to produce pseudopodia.

amphitrophic:

Organisms capable of gaining energy and nutrients by both autotrophic and heterotrophic means. (Same as amphizoic).

amphizoic:

See amphitrophic.

anoxic:

An environment in which there is no free oxygen present. A situation that commonly arises in natural habitats when the biological demand for oxygen exceeds the supply, for example in sediments or when a site is organically polluted.

apical:

Relating to the apex, the anterior pole.

apomorphy: (apomorphic, apomorphies)

A character state derived by evolution from an ancestral state (plesiomorphy). A novel evolutionary trait.
Also see synapomorphy, autapomorphy.

appressorium: (appressoria)

Specialized structure of a fungal filament that anchors to the surface of a plant root, facilitating the invasion of the plant by the fungus.

aquatic:

Pertaining to water - as in aquatic habitat (ponds, lakes, streams, oceans, etc).

arboreal: (arboreality)

Organisms living on or in trees, fequenting trees, or a part of an organism resembling a tree in form and branching structure.

Archezoa:

1990's but fluid concept for eukaryotes believed to have evolved before the origin of mitochondria. Over time, the group has included some or all of the entamoebae, microsporidia, diplomonads, retortamonads, oxymonads, trichomonads, hypermastigids, mastigamoebids, Pelomyxa, Phreatamoebae and trimastix in various combinations. For more information see the Discussion of Phylogenetic Relationships on the Eukaryotes page.

autapomorphy: (autapomorphic, autapomorphies)

A uniquely-derived character state. An apomorphy that is unique to a single terminal taxon.
Compare to synapomorphy.

autotrophic:

Organisms which trap energy from physical or chemical sources and use the energy to assemble the macromolecules of which they are made. Photosynthesis is the only process by which this happens in eukaryotes, but additional processes are found among prokaryote organisms. Compare with heterotrophic.

axoneme:

A geometrically packed assemblage of microtubules (subcellular scaffolding) used to support flagella, the arms of Heliozoa, etc.

bacterivore: (bacterivores)

An organism that eats bacteria.

bacterivorous: (bactivorous)

Said of bacterivores.

base pair: (base pairs)

A pair of nucleotides on opposite strands of a nucleic acid hydrogen-bonding with each other according to the pairing rules between a pyrine and a pyrimidine.

Batesian mimicry: (Batesian mimic)

A palatable/harmless mimic resembling an unpalatable/vigilant model.
Batesian mimicry postulates that palatable mimics are likely to gain protection from predators that have learned to avoid the unpalatable/vigilant model as long as the mimic remains relatively rare compared to the model.

bathypelagic: (bathypelagic zone)

The part of the ocean that extends down from 1000m to 4000m. No sunlight reaches this zone so it is very cold and completely dark. It is also characterized by very high water pressure.

benthos: (benthic, benthic zone)

The bottom sediments of the sea, rivers, lakes, ponds, etc.

biotroph: (biotrophic, biotrophs)

An organism which is dependent on a living host organism as a source of nutrients.

bivittate:

Having a pair of longitudinal stripes.

black mud:

Reduced muds found below the surface of sediments in lakes and rivers. The blackness is caused by the occurrence of metal sulphides.

branch: (branched, branching, branches)

1. A secondary woody stem or limb growing from the trunk, main stem, or another secondary limb of a tree, shrub or vine.
2. Many other, subdivided, elongated structures of organisms resembling a tree branch.
3. Graphical representation of an evolutionary lineage in a phylogenetic tree diagram.

buccal:

Relating to structures associated with the mouth.
From Latin bucca, mouth cavity.

Burgess Shale:

The Burgess Shale is a sedimentary rock formation located in Yoho National Park, British Columbia, Canada. It contains exquisitely preserved fossils of invertebrate animals that lived on the seafloor 505 to 500 million years ago, during the Cambrian period.

For more information see Burgess Shale at The Paleontology Portal.

Cambrian:

The Cambrian is the earliest period of the Paleozoic era, spanning the time between 543 and 490 million years ago.

For more information see The Cambrian at The Paleontology Portal.

Carboniferous:

The Carboniferous is a period of the Paleozoic era, spanning the time between the Devonian and the Permian, about 354 to 290 million years ago.

For more information see The Carboniferous at The Paleontology Portal.

carnivory: (carnivore, carnivory, carnivores)

The consumption of living animal flesh.

carpel: (carpels)

The female reproductive organs at the center of a flower, consisting of the ovary, style, and stigma.

carpogonium: (carpogonia)

The female gamete-producing reproductive organ of red algae. It develops from the gametophyte.

carposporangium: (carposporangia)

A sporangium produced by a carposporophyte. The organ that contains the carpospore.

carpospore: (carpospores)

A nonmotile, diploid spore found in red algae. Carpospores are produced by mitosis at the tips of gonimoblast filaments and develop into the tetrasporophyte phase.

carposporophyte: (carposporophytes)

A morphological stage in the life cycle of some red algae. The sporophyte phase which results form the fertilization of the carpogonium. It consists of growths originating from a carposporangium.

cellulose polysaccharide:

Compound used to make walls (normally around the outside) of certain types of cell.

Cenozoic:

The Cenozoic era spans the time from the end of the Mesozoic, about 65 million years ago, to the present. It is generally subdivided into two periods, the Tertiary and the Quaternary.

character: (characters)

Any heritable attribute or feature of an organism that can be used for recognizing, differentiating or classifying a taxon.
Biologists use characters from a variety of different sources, including morphological, behaviorial, developmental, and molecular data.

character state: (character states)

Alternative forms of a character.

chlorophyll:

A family of pigments used in photosynthesis to trap radiant energy. Normally located with chloroplasts. Chloroplasts with chlorophyll b have a bright green colour, those with chlorophylls a and c are off-green or yellow.

chloroplast:

An organelle found in eukaryotic algae and plants (and occasionally as symbionts in certain protist and animal cells). The site of photosynthesis and of chlorophyll.

chromist: (chromophyte, chromists, chromophytes)

A term used variously to refer to some or all of those algae with chloroplasts having chlorophylls a and c (i.e. stramenopiles, cryptomonads, and haptophytes). The cluster is probably polyphyletic.

chromosome: (chromosomes)

A long strand of eukaryotic DNA, often complexed with specialized proteins called histones.

cilium: (cilia)

A behavioural type of eukaryotic flagellum, distinctive because they occur in large numbers, have a co-ordinated behaviour, and usually direct fluids parallel to the surface.

clade: (clades)

A single complete branch of the Tree of Life; more formally, a monophyletic group of organisms.

classification: (classifications)

The practice of arranging organisms in named groups (taxa).

coccoid:

Rounded in shape, ball-like.

coelom: (coelomate, coelomic)

A fluid-filled body cavity in animals, lined with tissue of mesodermal origin, housing the internal organs.

commensal:

An organism that derives nourishment or shelter by living in close association with another organism (the host), without damaging the host.

conjugation:

A type of sexual event during which two cells fuse. It may or may not lead to reproduction.

conspecific: (conspecifics)

A member of the same species.

containing group:

A given group's containing group is that group in which this group is included as a subgroup.
Any group in the Tree of Life has a series of hierarchically nested containing groups going all the way down to the ultimate containing group, Life on Earth.

contractile vacuole:

Part of the contractile vacuole complex, often the only part that is visible with the light-microscope. It collects fluid and periodically allows the fluid to be discharged through the cell surface.

contractile vacuole complex:

An organelle involved in osmoregulation in protist cells, including contractile vacuole, spongiome (a membranous system not usually visible with the light microscope), possibly a pore, collecting canals and ampullae.

convergence: (convergent, convergences)

In general, two or more things coming closer together.

Convergent Evolution

Evolution of similarities in unrelated groups of organisms.
Adaptation for similar function may lead to novel characteristics (homoplasies), which are similar, although they are not inherited from a common ancestor. In some cases, such similarities may be superficial, as in the wings of birds, bats, and insects. In others, similarities can be so striking that it is difficult to determine that the traits arose independently and then later converged upon their current form.

corolla:

Collective term for the petals of a flower.

crenulated:

A surface with a regularly indented margin.

crepuscular:

An adjective used to describe things relating to the twilight associated with sunrise and sundown. An organism is considered to be crepuscular if it is active primarily during the dawn and dusk hours. Compare to diurnal, nocturnal.

Cretaceous:

The Cretaceous is the final period of the Mesozoic era, spanning the time between about 144 to 65 million years ago.

For more information see The Cretaceous at The Paleontology Portal.

crista: (cristae)

Fold of the inner membrane of mitochondria.

cryptogam: (cryptogams)

Nineteenth century concept broadly covering small algae, fungi, and bacteria.

cytopharynx:

Part of the food ingestion structures (mouth) of some cells; usually a channel of microtubules that draws newly formed food vacuoles away from the cytostome and into the cell.

cytoplasm:

The matter which makes up cells, within which organelles occur.

cytoproct:

Found in some ciliates, the site at which old food vacuoles fuse with the cell surface, and undigested residues are excreted.

cytoskeleton:

Intracellular components used to provide shape to a cell or to create tracts along which cellular organelles may be moved, mostly comprised of microtubules and actin filaments.

cytostome:

Literally, 'the cell mouth'. only used in reference to organisms which ingest food at one or more particular locations, and then best used in reference to the region(s) of the cell surface through which food gains entry into the cell; part of the 'mouth' structures; see also cytopharynx.

daughter cells:

The products of cell division of protists.

dehiscence: (dehisce, dehiscent, dehisces)

Breaking open at maturity, along a definite line, to release materials (e.g., seeds, spores).

deletion: (deletions)

Loss of one or more nucleotides from a nucleic acid sequence.

demersal:

Living on or near the bottom of a body of water.

detritivore: (detritivorous, detritivory, detritivores)

An organism that eats detritus.

detritus:

Fragments of dead plant and animal material before, during and after breakdown by agents of decay. May incorporate inorganic matter (such as mud).

Devonian:

The Devonian is a period of the Paleozoic era, spanning the time between the Silurian and the Carboniferous, about 417 to 354 million years ago.

For more information see The Devonian at The Paleontology Portal.

dichotomous tree:

A tree where all branching points are dichotomies. That is, a tree is dichotomous if at each branch point there are only two immediate descendents. This is in contrast to a polytomous tree.

dichotomy: (dichotomies)

A branch point on a tree that has two immediate descendents.

diffusion feeding:

Feeding strategy in which the predator relies on the movements of the prey to make contact - as in heliozoa and suctoria.

diploid: (diploidy, diploids)

Diploid organisms have diploid cells. Diploid cells have two copies of each chromosome.

distal:

Away from (contrast with proximal).

diurnal:

An organism that is active during the daytime rather than at night.

DNA: (deoxyribonucleic acid)

Long molecule in the nucleus of cells, shaped like a double-helix, contains the genetic information that determines the development and functioning of an organism's cells.

ectoparasitoid: (ectoparasitoids)

A parasitoid that lays its eggs on the surface of the host. Larvae feed on the host from the outside.

ectosymbiotic:

Organism living on the surface of another organism.

ejectisome:

A type of explosive extrusome found in cryptoflagellates.

endemic: (endemism, endemics)

A group of organisms that is restricted to a particular geographic area.

endoparasitoid: (endoparasitoids)

A parasitoid whose immature stages live inside the body of its host.

enzyme: (enzymes)

A protein that acts as a catalyst, accelerating the rate of specific biochemical reactions.

epithelium: (epithelial, epithelia)

Tissue covering or lining of the surface of an organism or an organ, both external and internal. Examples include the skin cells, the inner linings of the lungs, blood vessels, and the digestive tract, etc. Epithelial cells are generally tightly packed, providing a continuous barrier protecting the underlying cells.

evolution: (biological evolution, evolutionary, evolve, evolving, organic evolution)

Genetic changes in lineages of organisms over time. Through this process, a lineage may split and diversify into new species.

For a good introduction to evolution, see Evolution 101 at the Understanding Evolution web site.

exoskeleton:

A supportive structure lying outside the cell or body.

extracellular:

Outside the cell.

extrorse:

Facing outward, away from the axis or center.

extrude:

To push out.

extrusome:

A kind of organelle, the contents of which can be extruded, for example to catch or kill prey or for protection.