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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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.
Relating to position: toward the mouth (cf. aboral).
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.
No lorica present.
amino acid: (amino acids)
Molecule that serves as the basic structural unit of proteins. General formula: R–CH(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.
Like an amoeba. Usually means that the organism has the capacity to produce pseudopodia.
Organisms capable of gaining energy and nutrients by both autotrophic and heterotrophic means. (Same as amphizoic).
See amphitrophic.
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.
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.
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.
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.
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.
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.
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.
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.


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.


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.

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

insect hierarchy

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.
Collective term for the petals of a flower.
A surface with a regularly indented margin.
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.

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.
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.
The matter which makes up cells, within which organelles occur.
Found in some ciliates, the site at which old food vacuoles fuse with the cell surface, and undigested residues are excreted.
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.
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.
Living on or near the bottom of a body of water.
detritivore: (detritivorous, detritivory, detritivores)
An organism that eats detritus.
Fragments of dead plant and animal material before, during and after breakdown by agents of decay. May incorporate inorganic matter (such as mud).

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.

dichotomy diagram

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.
Away from (contrast with proximal).
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.
Organism living on the surface of another organism.
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.

A supportive structure lying outside the cell or body.
Outside the cell.
Facing outward, away from the axis or center.
To push out.
A kind of organelle, the contents of which can be extruded, for example to catch or kill prey or for protection.
extrusopodium: (extrusopodia)
Pseudopodia which bear extrusomes.
Capable of reproduction.
filament: (filamentous, filaments)
A thin strand. May refer to the appearance of an organism, a part of an organism, or a strand of cytoplasm.
In angiosperms: the slender, thread-like stalks that make up the stamens of a flower.
filose pseudopodium: (filose pseudopodia)
Pseudopodia that are thin and threadlike but without internal skeletal elements
flagellate: (flagellates)
A kind of protist bearing flagella; a very diverse group with unclear boundaries. distinguished from ciliates because flagella are few in number, and usually create a thrust along the length of the organelle rather than parallel to the body surface.
The siliceous lorica of a diatom.
gametophyte: (gametophytes)
The phase of the life cycle of sexually reproducing plants and algae in which the gametes (egg and sperm) are produced. The gametophyte arises from the germination of a haploid spore.
gene: (genetic, genes)
Functional and physical unit of inheritance that is passed from parent to offspring. Genes are pieces of DNA containing the code for the synthesis of a functional polypeptide or RNA molecule. Most genes contain coding regions (exons), non-coding sequences (introns), and transcription-control regions.
gonimoblast: (gonimoblasts)
Tissue derived from the the fertilized nucleus of some red algae, equivalent to the carposporophyte. It may develop from the carpogonium or an auxiliary cell, and it ultimately produces carposporangia by mitosis.
granule: (granules)
Solid inclusions in cells or items adhering to the surface of cells. Usually refractile, in that they may look bright when viewed with the microscope.
Green River Formation:

The Green River Formation, exposed in northwest Colorado, southwest Wyoming, and northeast Utah (USA), is what remains of a large lake that existed in the area about 60 to 38 million years ago. It contains one of the most complete fossil assemblages of plants, insects, reptiles, fish, and mammals in the world.

For more information see Green River Formation at The Paleontology Portal.

hadal: (hadal zone)
The very deepest parts of the ocean floor, including areas found in deep sea trenches and canyons. These areas are characterized by total darkness, constant cold, and very intense water pressure.
haploid: (haploidy, haploids)
Haploid organisms have haploid cells. Haploid cells have a single copy of each chromosome.
herbivory: (herbivore, herbivorous, phytophage, phytophagic, phytophagous, herbivores, phytophages)
The consumption of living plant material.
hermaphrodite: (hermaphroditic, hermaphrodites)
An organism which has both female and male reproductive organs and is therefore capable of producing both eggs and sperms. A simultaneous hermaphrodite has both kinds of reproductive organs at the same time. A sequential hermaphrodite has one kind early in life and the other later in life.
heterokont: (heterokonts)
A term used variously to refer to some or all of those algae with chloroplasts having chlorophylls a and c (i.e. stramenopiles, cryptomonads, haptophytes and dinoflagellates). The group is paraphyletic as it fails to include some taxa derived from heterokonts.
A mode of nutrition in which the consumer relies upon molecules created by other organisms for energy and nutrients. Either osmotrophic (absorbing soluble organic matter) or phagotrophic (ingesting particles of food).
A class of proteins found in eukaryotic chromosomes. Histones bind with DNA and compact it, so that it will fit inside the nucleus.

The Holocene (or Recent) is the second epoch of the Quaternary period, spanning the time between about 11,000 years ago and the present.

Organisms that remain pelagic throughout their entire life cycle.
homology: (homologous, homologies)

A characteristic shared by different groups of organisms that is derived from the same structure or trait in their common ancestor.

Ancestral characteristics may be greatly modified in descendent groups, so that homologous traits may not be similar in appearance or function. Clues of their common ancestry may often be found in structural details, ontogeny, or position relative to other features.

cf. homoplasy, convergent evolution.

For more information about homologies see Homologies and Analogies and Recognizing Homologies on the Understanding Evolution web site.

homoplasy: (analogous, analogy, homoplasic, homoplastic, analogies, homoplasies)

A similiarity between different groups of organisms that is not homologous (due to common ancestry) but rather the result of convergent evolution or character reversal.

cf. homologies

For more information about homoplasies (analogies) see Homologies and Analogies on the Understanding Evolution web site.

horizontal gene transfer: (horizontal transfer, lateral gene transfer, lateral transfer, horizontal transfers, lateral gene transfers, lateral transfers)
A natural process by which some of the genes of an organism are transferred and incorporated into the genome of an organism belonging to another species. This contrast with vertical gene transfer, in which the genes of an organism are passed on to its offspring.
host: (hosts)
An organism that provides nourishment and/or shelter to another organism, e. g., a commensal or a parasite.
hydrolysis: (hydrolytic, hydrolyses)
The breaking apart of a molecule by addition of water.
hypha: (hyphae)
Microscopic, tubular filaments that make up the body of a multicellular fungus.
A term used to refer to premitochondriate eukaryotes.
idiobiont: (idiobionts)
A parasitoid that paralyses and arrests the development of its host. Compare to koinobiont.
A structure produced by the organism, as opposed to a xenosome or foreign body. Used to refer to the elements which make up or adhere to the test of some amoebae.
Not moving, sometimes used to refer to cells which are fixed to the substrate.
In phylogenetic analyses, the subgroups of the group whose phylogeny is reconstructed.
Compare to outgroup.
inheritance: (inherited, inheriting)
The process of genetic transmission of characteristics from parents to offspring.
interspecific: (interspecies, interspecifically)
Arising or occurring between species.
Compare to intraspecific.
intraspecific: (intraspecies, intraspecifically)
Arising or occurring within a species, involving the members of one species.
Compare to interspecific.

The Jurassic is a period of the Mesozoic era, spanning the time between the Triassic and the Cretaceous, about 206 to 144 million years ago.

For more information see The Jurassic at The Paleontology Portal.

koinobiont: (koinobionts)
A parasitoid that permits its host to continue to feed, grow, and function after parasitism. Compare to idiobiont.
lineage: (lineages)
A group of organisms, cells, or genes linked to one another through a continuous line of descent, i. e., through parent-offspring connections.
When a fruit capsule dehisces along lines coinciding with the centers of loculi (the enclosed compartments within the ovary). Compare: septicidal.
loculus: (locular, locule, locules, loculi)
A small cavity or hollow space within an organism or in an organ.
An organic or inorganic casing or shell incompletely surrounding an organism, usually loose fitting.
macronucleus: (macronuclei)
One of two types of nuclei found in ciliates. Typically the larger of the two, may be rounded, like a long sausage, or like a string of beads. Involved in production of proteins but not in sexual reproduction. Essential for the day to day activities of the ciliate (see micronucleus).
Pertaining to the sea.
Projection of a cell that supports one or more flagella
A compound structure comprised of many cilia and associated with the mouth of a ciliate. Either present in groups of three (oligohymenophora) or as a band of many more (polyhymenophora).
mesopelagic: (mesopelagic zone)
The mid-ocean zone at depths between about 180 and 900 meters (600 and 3,000 feet). Also called the "twilight" zone because it is found between the well-lit photic zone above and the darkness of the deep ocean below.

The Mesozoic era spans the time from the end of the Paleozoic, about 248 million years ago, to the beginning of the Cenozoic, about 65 million years ago. It is generally subdivided into three periods: Triassic, Jurassic, and Cretaceous.

micronucleus: (micronuclei)
One of two kinds of nuclei found in ciliates, dividing to produce two similar nuclei during asexual reproduction and producing nuclei with half the complement of dna for sexual activity. usuaully the smaller of the two types of nuclei, but many may be present. some cells lack a micronucleus and survive quite well without it.
microorganism: (micro-organism, microbe, microbial, micro-organisms, microbes, microorganisms)
Usually single-celled creature that is too small to be seen without the aid of a microscope. The term may be applied to bacteria, archaea, and viruses, as well as certain fungi and protists.
microtubule: (microtubules)
A subcellular structure comprised of the protein tubulin and used for support - part of the cytoskeleton. Individual microtubules cannot be seen by conventional light-microscopy, but aggregates of microtubules can.
mimicry: (mimic)
Resemblance of an organism (the mimic) in appearance and/or behavior to another organism or object (the model).
See Müllerian mimicry, Batesian mimicry
mitochondrion: (mitochondria, mitochondrions)
Site of aerobic respiration (energy production that is dependent on oxygen) in eukaryotic cells.
Used in reference to organisms which use a mixture of nutritional strategies, such as organisms with chloroplasts and carry out photosynthesis but are also able to feed by phagocytosis.
monophyletic: (monophyly)
A group of organisms that includes their most recent common ancestor and all of its descendents. (cf. paraphyletic, polyphyletic)

monophyletic diagram

morphology: (morphological)
The study of the form and structure of an organism or one of its body parts. The word is sometimes used to also mean the form or structure itself.
Moving, for example by swimming, gliding, crawling, jumping, or kicking. Part of the body (e.g., cilia) may be motile in a cell which is not motile and is fixed in one position.
Made of, or with the texture of, mucus
A gelly-like substance produced by organisms, texture may vary from virtually fluid to stiff and rubber-like.
An organism consisting of more than one cell.
Müllerian mimicry: (Müllerian mimic)
Resemblance among several unpalatable/vigilant species.
The Müllerian mimicry theory postulates that several species mimic each others' warning signal in order to more effectively train predators to avoid eating individuals displaying the shared signal.
Stiff aggregates of many microtubules found around the cytostome of some ciliates and used during the ingestion of food. A type of ingestion rod.
A term referring to ocean waters from the low-tide mark to the edge of the continental shelf at a depth of about 200 meters. The neritic zone is characterized by low water pressure, plenty of sunlight, and stable temperatures.
neuston: (neustonic)
The environment of the interface between water and air, often rich in bacteria and protists.
An organism that is active at night rather than during the day.
node: (nodes)
A branching point in a phylogenetic tree, representing the common ancestor of the lineages descending from this branching point.
Having a nucleus.
nucleolus: (nucleoli)
An optically dense region (or regions) in a nucleus, associated with RNA synthesis. Not always visible.
nucleotide: (nucleotides)
Molecule that serves as the basic structural unit of nucleic acids like DNA and RNA. Each nucleotide consists of three other molecules — a sugar, a phosphate group, and a purine or pyrimidine base.
nucleus: (nuclei)
An organelle found only in eukaryotic cells, in which most of the cellular DNA (genetic material) is located. Most cells have a single nucleus, but certain species may have many nuclei.
nudipodium: (nudipodia)
A type of unsupported pseudopodium without evident extrusomes (compare extrusopodia).
ontogeny: (ontogenesis, ontogenetic, ontogenies)
The developmental history of an individual organism from its origin to its death.

The Ordovician is a period of the Paleozoic era, spanning the time between the Cambrian and the Silurian, about 490 to 443 million years ago.

For more information see The Ordovician at The Paleontology Portal.

organelle: (organelles)
A discrete structure found within eukaryotic cells.
organism: (organismal, organisms)
Any living creature. A plant, animal, or micro-organism.
A form of nutrition in which soluble compounds are taken up by the organism, either by pinocytosis or by mechanisms capable of transporting one or a few molecules at a time (membrane pumps).
ossicle: (ossicular, ossiculum, ossicles)
Vertebrates: a small bone.
Echinoderms: small calcareous plates forming the skeleton.
outgroup: (outgroups)
A taxon that is not part of the ingroup but that is included in a phylogenetic analysis in order to provide information about the root of the ingroup and to help differentiate between apomorphies and plesiomorphies in the ingroup.
oviposition: (oviposit, ovipositing, oviposits)
The deposition of eggs by the mother into a host or the environment.
ovipositor: (ovipositors)
A tubular organ that is used for oviposition, i. e., the laying of eggs. In some insects, especially parasitoid wasps, the ovipositor can be very long.
Paleozoic: (Palaeozoic)

The Paleozoic era spans the time from the end of the Precambrian, about 543 million years ago, to the beginning of the Mesozoic, about 248 million years ago. It is generally subdivided into six periods: Cambrian, Ordovician, Silurian, Devonian, Carboniferous, and Permian.

paraphyletic: (paraphyly)
A group of organisms that includes their most recent common ancestor and some but not all of its descendents. (cf. monophyletic; technically speaking, the distinction between polyphyletic and paraphyletic is not as clear as it might seem.)

paraphyletic diagram

parasitism: (parasite, parasitic, parasites)
An interaction between organisms in which one organism (the parasite) lives in or on the living tissue of another organism (the host), deriving nutrients at the expense of the host. Parasites usually live for some time in association with their hosts rather than killing them soon after encounter.
parasitoid: (parasitoids)
An organism that is parasitic on a single host in its immature stages, usually kills its host at some point during its development, and is free-living as an adult. Most known parasitoids are insects, in particular wasps (Ichneumonidae, Chalcidae), flies (Tachinidae), and strepsipterans (Stylopidae).
paraxial rod:
A rod of material lying within the flagellum parallel to the axoneme, only found in some protists (e.g. euglenids) causing the flagellum to appear relatively thick.
Pertaining to the water column of the open sea - as opposed to coastal areas or the sea floor.
The outer region of cytoplasm of some protozoa, the term is applied only when the region can be distinguished because it appears to be relatively stiff and highly structured. Used mostly in reference to euglenids and ciliates.
The entire assemblage of scales, spines and spicules which encase some heliozoa, chrysomonads, etc.
Regular contractions of a body or part of a body. Mostly said of the intestinal system of vertebrates but also the squirming behaviour of some euglenids.
The region of the body around, and external to, the mouth. To deserve application of this term, the region must be modified to favour the acquisition of food.

The Permian is the final period of the Paleozoic era, spanning the time between about 290 to 248 million years ago.

For more information see The Permian at The Paleontology Portal.

petal: (petals)
The most conspicuous organs of a flower, often brightly colored, providing chemical and visual signals as well as landing platforms for pollinators. They are sterile and surround the fertile organs.
The ingestion of visible particles of food by enclosing them with a membrane to form a food vacuole.
An organism which feeds by phagocytosis.
A region of the ingestion apparatus lying internal to the mouth (of a metazoan organism) or internal to the cytostome of a protist. Involved in the swallowing process (see cytopharynx).
photic: (photic zone)
The upper zone of a body of water (a lake or an ocean) that is penetrated by sufficient sunlight to allow for photosynthesis.
The products of photosynthesis.
A means of acquiring energy for metabolism which involves trapping radiant energy in chloroplasts, the use of that energy to break up water molecules (hydrolysis) and to convert released energy into an accessible form - such as the molecule ATP. The only form of autotrophy in eukaryotic cells. Some heterotrophic protists have symbiotic algae which allow them to exploit photosynthesis.
photosynthetic pigments:
Large molecules in chloroplasts that absorb radiant energy (hence they have colour), mostly chlorophylls and carotenes and, occasionally phycobilins.
phylogenetic inference:
The scientific process of collecting and analyzing data to provide the best estimate of the true phylogeny of a group of organisms.
The scientific discipline of resolving phylogenetic relationships between organisms.
phylogeny: (phylogenetic)

The evolutionary history of a group of organisms.

Any group of species are descended from a common ancestral species, which, over time, split into two species, with these descendents splitting again, and again, until the entire collection of species was produced through evolution and speciation (the splitting of a lineage). The genealogical connections thereby formed in general take the shape of a tree, called the phylogeny of the group.

For more information about this topic have a look at our What is Phylogeny? page and check out the Understanding Evolution web site, in particular the section about Understanding Phylogenies.

A process of ingesting material by enclosing it with a membrane. The resulting structure is usually too small to be seen with the light microscope and is mostly suitable for the ingestion of fluid or mucus.
plankton: (planktonic)
Organisms living in the water column (above the sediment).
plasmodium: (plasmodia)
A type of amoeboid organization involving a large mass of cytoplasm and, usually, many nuclei. A type of body form adopted by some slime moulds. The genus Plasmodium is the cause of malaria.
plastid: (aplastidic, plastidic, plastids)
The same as chloroplast, from it come the terms aplastidic and plastidic for with and without chloroplasts respectively.

The Pleistocene is an epoch of the Quaternary period, spanning the time between about 1.8 million years ago and the beginning of the Holocene about 11,000 years ago.

plesiomorphy: (plesiomorphic, plesiomorphies)
An ancestral character state. A trait from which an evolutionary novelty (apomorphy) is derived.
Also see symplesiomorphy.
polypeptide: (polypeptides)
A chain of amino acids, usually less than 100 amino acids in length. Polypeptides are the building blocks of proteins.
polyphagous: (polyphage, polyphagy, polyphages)
Feeding on many different kinds of food. In the case of parasites or parasitoids, the use several different groups of organisms as hosts.
A group of organisms that does not include their most recent common ancestor. (cf. monophyletic; technically speaking, the distinction between polyphyletic and paraphyletic is not as clear as it might seem.)

polyphyletic diagram

polytomous tree:
A tree that has at least one branch point that is a polytomy. A tree with only one polytomy is called polytomous, as is a tree with multiple polytomies. This is in contrast to a dichotomous tree.
polytomy: (polytomies)
A branch point on a tree that has more than two immediate descendents.

polytomy diagram


The Precambrian is the time period from the beginning of Earth, about 4.5 billion years ago, to the beginning of the Paleozoic era, about 543 million years ago.

For more information see The Precambrian at The Paleontology Portal.

predation: (predaceous, predacious, predator, prey, predators)
An interaction between organisms in which one organism, the predator, kills and eats the other organism, the prey.
prokaryote: (procaryote, procaryotic, prokaryotic, procaryotes, prokaryotes)
Unicellular organisms lacking a membrane-bound, structurally discrete nucleus and membrane-bound organelles. The term is generally applied to bacteria and archaea. Not a monophyletic group.
protein: (proteins)
A large molecule composed of amino acid chains. Proteins perform a wide variety of cellular functions. Examples are hormones, enzymes, and antibodies.
protist: (Protista, protists)
A paraphyletic group consisting of those eukaryotes which are not animals, true fungi or green plants.
protozoan: (Protozoa, protozoans)
From a phylogenetic point of view, an outmoded concept because it included unrelated eukaryotes - various amoebae, flagellates, ciliates and sporozoa
Near to (compare distal).
pseudopodium: (pseudopodia)
Transient extensions of the cell surface, used for locomotion or feeding. They may be supported internally (actinopods) or not (rhizopoda), they may be thread like (filose) or broad (lobose), may or may not bear extrusomes (nudipodia, extrusopodia) and they may be one (monopodial) to many (polypodial) produced at one time.
With a dimpled or spotted appearance.
A system involving a sac and channels and found in some dinoflagellates. The function is not understood, but it may act as an osmoregulatory organelle.
pyrenoid: (pyrenoids)
A protein body lying inside some types of chloroplasts.

The Quarternary is the second period of the Cenozoic era, spanning the time between about 1.8 million years ago and the present. It is generally subdivided into two epochs, the Pleistocene and the Holocene.

For more information see The Quarternary at The Paleontology Portal.

reversal: (character reversal)
The re-establishment of an ancestral character state through the loss of an evolutionary novelty (apomorphy). For example, winged insects (Pterygota) evolved from a wingless ancestor; however, some pterygote lineages have subsequently lost their wings, e.g., fleas, lice, some grasshoppers and beetles.
rheotaxis: (rheotactic)
Movement of an organism in response to the motion of a current of water or air.
rheotropism: (rheotropic)
Growth or orientation of an organism, or of part of an organism, in response to the motion of a current of water or air.
RNA: (ribonucleic acid)
A molecule found in the nucleus and cytoplasm of cells. It plays an important role in protein synthesis and other chemical processes of the cell. The structure of RNA is similar to that of DNA. There are several classes of RNA molecules, including messenger RNA, transfer RNA, ribosomal RNA, and other small RNAs, each serving a different purpose.
root: (rooted, rooting, roots)

The below ground portion of a plant.

The root of a subtree of the Tree of Life is the branch that connects the subtree to the remainder of the Tree of Life. For a given group of organisms, the root is the branch that connects this group to its containing group. root diagram

sepal: (sepals)
The leaf-like, outermost organs of a flower. They are sterile and protect the fertile parts of the developing flower.
When a fruit capsule dehisces along lines coinciding with the partitions between loculi (the enclosed compartments within the ovary). Compare: loculicidal.
sequence alignment:
Procedure for the linear comparison of two or more molecular sequences in order to identify those positions that are likely to have a common evolutionary origin. Series of characters that are in the same order in the sequences are used as reference points, and hypothetical gaps may be inserted in order to make similar regions line up with one another.
Refers to organisms which are fixed to the substrate, for example by means of a stalk or lorica.
Incoporating silica.

The Silurian is a period of the Paleozoic era, spanning the time between the Ordovician and the Devonian, about 443 to 417 million years ago.

For more information see The Silurian at The Paleontology Portal.

sister group: (sister taxon, sister groups, sister taxa)
The two groups resulting from the splitting of a single lineage.
A contractile element in the stalk of some peritrich ciliates.

The splitting of an evolutionary lineage producing (usually) two new, separate species, which thus begin their own, unique evolutionary histories.

For more information about speciation and its significance in evolution check out the Understanding Evolution web site's pages about Speciation.


A leaf on the tree of life. A group of organisms that share a common gene pool as well as a unique evolutionary history distinct from other groups of organisms.

The definition of a species is more difficult than one might think. Over the years, a variety of different species concepts have been proposed, and the debate about the most appropriate definition is ongoing. Check out Defining a Species on the Understanding Evolution web site for more information.

spicule: (spicules)
Delicate pointed structures lying external to the body and usually pointed away from it. Like spines, but invariably excreted and more delicate.
having sporangia
A stalk bearing one or more sporangia.
sporangium: (sporangial, spore case, spore receptacle, spore sac, sporangia)
An organ that contains or produces spores. Found in plants, fungi, algae.
spore: (spores)
Unicellular body produced by plants, fungi, and some microorganisms. Often a resting stage, encased in a protective coat, adapted to resist heat, desiccation, or other unfavorable environmental conditions. Spores can give rise to a new individual either directly or after fusion with another spore.
sporophyte: (sporophytes)
The phase of the life cycle of sexually reproducing plants and algae in which the spores are produced. The sporophyte arises from the diploid zygote.
The process of spore development.
stamen: (staminate, stamens)
The male reproductive organs of a flower. They produce pollen and usually consist of slender, thread-like stalks (filaments) topped by pollen-bearing anthers.
standard length: (SL)
The length of a fish measured from the tip of the snout to the end of the fleshy part of the body. This measurement is preferred by many ichthyologists because it ignores the tail fin, which can often be damaged in specimens.
starch grain: (starch grains)
A term used loosely to refer to refractile masses of polysaccharides which are accumulated as storage products in the cell.
Incapable of reproduction.
stomatocyst: (stomatocysts)
A type of cyst, with a siliceous wall and a single plugged opening, formed by some chrysomonads (stramenopiles).
suspension feeding:
Feeding on suspended particles. The most usual ploy is filter-feeding, but not all suspension feeders feed in this way.
symbiosis: (symbiont, symbiotic, symbionts, symbioses)
Living in association with another organism, normally to the mutual advantage of both or to the advantage of one - the other being unaffected. Where there is a notable discrepancy in size, the term 'symbiont' is used to refer to the smaller member of the association which may occur inside (endosymbiont) or on the outside surface (ectosymbiont) of the larger member 'host'.
sympatry: (sympatric)
Species or populations occupying the same geographic area. Compare to allopatry.
symplesiomorphy: (symplesiomorphic, symplesiomorphies)
A shared ancestral character state (plesiomorphy). A trait that is shared by two or more groups due to inheritance from a distant common ancestor.
Symplesiomorphies are common to all the descendants of a distant common ancestor, and they cannot be used to infer close evolutionary relationships between subsets of these descendants.
synapomorphy: (synapomorphic, synapomorphies)
A shared derived character state (apomorphy). A novel evolutionary trait that is shared by two or more groups due to inheritance from an immediate common ancestor.
Synapomorphies are used by phylogenetic biologists to infer close evolutionary relationships between organisms.
syncytium: (syncitium, syncitia, syncytia)
Multinucleated mass of cytoplasm.
taxon: (taxa)
Any named group of organisms.
tendril: (tendrils)
A slender climbing organ by which some twining plants attach themselves to an object for support, formed by modification of a part of a plant, e.g. a stem, a leaf or leaflet, a stipule.
terminal taxon: (terminal taxa)
The taxa or named groups at the tips of the branches of a tree.

terminal taxa diagram

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

The Tertiary is the first period of the Cenozoic era, spanning the time between about 65 to 1.8 million years ago.

For more information see The Tertiary at The Paleontology Portal.

tetrasporangium: (tetrasporangia)
A unicellular sporangium containing four asexual tetraspores which are produced from meiosis. Tetrasporangia are found in certain red algae.
A layer which encloses a body, may refer to a closely adpressed rigid wall, or to a more loosely-attached rigid lorica or test or even to a soft enclosing sheath of material.
A form adopted by some species of ciliates that typically does not feed but moves quickly. May be thought of as an adaptation in response to a lack of food and the task of which is to hunt out new sources of food.

The Triassic is the earliest period of the Mesozoic era, spanning the time between about 248 to 206 million years ago.

For more information see The Triassic at The Paleontology Portal.

A type of extrusome which, when extruded, takes the form of a fine stiff filament. Typical of Paramecium, but used inadvertently to refer to other types of extrusomes.
troglobite: (troglobitic, troglobites)
An organism that is an obligate inhabitant of caves and underground water systems. Subterranean life often results in a series of characteristic morphological and physiological adaptations (troglomorphies) such as loss of pigment, blindness, and elongation of appendages.
troglomorphy: (troglomorphic, troglomorphies)
Morphological characteristics often exhibited by troglobites due to adaptation to life in caves and subterranean water systems. Examples include blindness, a loss of skin pigment, and elongation of appendages.
Said of organisms which are active and feeding, and contrasts with the encysted state, theronts, or swarmers. May also be used to refer to those aspects of metabolism associated with growth
undulipodium: (undulipodia)
A term preferred by some workers, usually in the US, for eukaryotic cilia and flagella.
Consisting of but a single cell.
vacuole: (vacuoles)
A structure in a cell enclosed by a membrane. Usually food vacuoles (associated with the digestion of food) or contractile vacuoles (association with the excretion of fluid). Small vacuoles may be called vesicles.
xenosome: (xenosomes)
A foreign body. Used to refer both to bits of debris which may be incorporated into the shells of some testate amoebae, and also to symbiotic algae lying inside other cells. Probably best restricted to the first use.
xylophagous: (xylophage, xylophagy, xylophages)
Feeding on wood.

Tree of Life Features

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