biology of trees
aboral
Relating to position
away from the mouth (cf. adoral).
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).
alga
(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. Also view or see Algae
Protists with Chloroplasts.
aloricate
No lorica present.
amoeba
(amoebae) Any of a polyphyletic grouping of organisms which move and feed using pseudopodia. Also view or 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
(apomorphies, apomorphic) A character state derived by evolution from an ancestral state (plesiomorphy). A novel evolutionary trait. Also see synapomorphy.
aquatic
Pertaining to water - as in aquatic habitat (ponds, lakes, streams, oceans, etc).
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. Also view or see the Discussion of Phylogenetic Relationships on the Eukaryotes page.
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.
benthic
Associated with the benthos.
benthos
The bottom sediments of rivers, lakes, ponds, etc.
black mud
Reduced muds found below the surface of sediments in lakes and rivers. The blackness is caused by the occurrence of metal sulphides.
buccal
Relating to structures associated with the mouth.
From Latin bucca, mouth cavity. carpel
(carpels)
The female reproductive organs at the center of a flower, consisting of the ovary, style, and stigma. cellulose polysaccharide
Compound used to make walls (normally around the outside) of certain types of cell. 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
(chromists, chromophytes, chromophyte)
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. coccoid
Rounded in shape, ball-like. 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. 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. convergent evolution
(convergence, convergent)
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. 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). detritivore
(detritivores, detritivorous, detritivory)
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). 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. distal
Away from (contrast with proximal). 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. ectosymbiotic
Organism living on the surface of another organism. ejectisome
A type of explosive extrusome found in cryptoflagellates. enzyme
(enzymes)
A protein that acts as a catalyst, accelerating the rate of specific biochemical reactions. epithelium
(epithelia, epithelial)
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. exoskeleton
A supportive structure lying outside the cell or body. extracellular
Outside the cell. 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. extrusopodium
(extrusopodia)
Pseudopodia which bear extrusomes. fertile
Capable of reproduction. filament
(filaments, filamentous)
A thin strand. May refer to the appearance 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. frustule
The siliceous lorica of a diatom. gene
(genes, genetic)
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. 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. herbivore
(herbivores, herbivorous, herbivory)
An organism that eats plants. 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. heterotrophic
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). histone
A class of proteins found in eukaryotic chromosomes. Histones bind with DNA and compact it, so that it will fit inside the nucleus. holopelagic
Organisms that remain pelagic throughout their entire life cycle. homology
(homologies, homologous)
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. homoplasy
(analogies, homoplasies, analogous, analogy, homoplastic)
A similiarity between different groups of organisms that is not homologous (due to common ancestry) but rather the result of convergent evolution. horizontal gene transfer
(horizontal transfers, lateral gene transfers, lateral transfers, horizontal transfer, lateral gene transfer, lateral transfer)
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
An organism that provides nourishment and/or shelter to a commensal or a parasite. hydrolysis
(hydrolyses, hydrolytic)
The breaking apart of a molecule by addition of water. hypha
(hyphae)
Microscopic, tubular filaments that make up the body of a multicellular fungus. hypochondria
A term used to refer to premitochondriate eukaryotes. idiosome
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. immotile
Not moving, sometimes used to refer to cells which are fixed to the substrate. lineage
(lineages)
A group of organisms linked to one another through a continuous line of descent, i. e., through parent-offspring connections. Biologists talk of lineages with respect to populations of organisms, cells, or genes. loculicidal
When a fruit capsule dehisces along lines coinciding with the centers of loculi (the enclosed compartments within the ovary). Compare
septicidal. loculus
(locules, loculi, locular, locule)
A small cavity or hollow space within an organism or in an organ. lorica
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). marine
Pertaining to the sea. mastigophore
Projection of a cell that supports one or more flagella membranelle
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). 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-organisms, microbes, microorganisms, micro-organism, microbe, microbial)
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, protists and viruses. 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. mitochondrion
(mitochondria, mitochondrions)
Site of aerobic respiration (energy production that is dependent on oxygen) in eukaryotic cells. mixotrophic
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) motile
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. mucilaginous
Made of, or with the texture of, mucus mucus
A gelly-like substance produced by organisms, texture may vary from virtually fluid to stiff and rubber-like. multicellular
An organism consisting of more than one cell. nemadesmata
Stiff aggregates of many microtubules found around the cytostome of some ciliates and used during the ingestion of food. A type of ingestion rod. neuston
(neustonic)
The environment of the interface between water and air, often rich in bacteria and protists. node
(nodes)
A branching point in a phylogenetic tree, usually representing the common ancestor of the lineages descending from this branching point. In the Tree of Life Project, each node represents this common ancestor and all of its descendents. nucleated
Having a nucleus. nucleolus
(nucleoli)
An optically dense region (or regions) in a nucleus, associated with RNA synthesis. Not always visible. 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). organelle
(organelles)
A discrete structure found within eukaryotic cells. osmotrophic
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). 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.) parasite
(parasites, parasitic)
An organism that 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 killing them soon after encounter. 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. pelagic
Pertaining to the water column of the open sea - as opposed to coastal areas or the sea floor. pellicle
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. periplast
The entire assemblage of scales, spines and spicules which encase some heliozoa, chrysomonads, etc. peristalsis
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. peristome
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. 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. phagocytosis
The ingestion of visible particles of food by enclosing them with a membrane to form a food vacuole. phagotroph
An organism which feeds by phagocytosis. pharynx
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). photosynthates
The products of photosynthesis. 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. 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 so on, until the entire collection of species was produced. The genealogical connections thereby formed in general take the shape of a tree, called the phylogeny of the group. pinocytosis
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
(plastids, aplastidic, plastidic)
The same as chloroplast, from it come the terms aplastidic and plastidic for with and without chloroplasts respectively. plesiomorphy
(plesiomorphies, plesiomorphic)
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.
polyphyletic
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.)
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.
prokaryote
(procaryotes, prokaryotes, procaryote, procaryotic, prokaryotic) 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
proximal
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.
punctate
With a dimpled or spotted appearance.
pusule
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.
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
(roots) The below ground portion of a plant. The root of a piece of the Tree of Life is that branch that connects to the remainder of the Tree; that is, it is the branch that connects to the containing group.
sepal
(sepals) The leaf-like, outermost organs of a flower. They are sterile and protect the fertile parts of the developing flower.
septicidal
When a fruit capsule dehisces along lines coinciding with the partitions between loculi (the enclosed compartments within the ovary). Compare
loculicidal.
sessile
Refers to organisms which are fixed to the substrate, for example by means of a stalk or lorica.
siliceous
Incoporating silica.
sister group
(sister groups, sister taxa, sister taxon) The two groups resulting from the splitting of a single lineage.
spasmoneme
A contractile element in the stalk of some peritrich ciliates.
spicule
(spicules) Delicate pointed structures lying external to the body and usually pointed away from it. Like spines, but invariably excreted and more delicate.
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.
sporulation
The process of spore development.
stamen
(stamens, staminate) The male reproductive organs of a flower. They produce pollen and usually consist of slender, thread-like stalks (filaments) topped by pollen-bearing anthers.
starch grain
(starch grains) A term used loosely to refer to refractile masses of polysaccharides which are accumulated as storage products in the cell.
sterile
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
(symbionts, symbioses, symbiont, symbiotic) 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'.
symplesiomorphy
(symplesiomorphies, symplesiomorphic) 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
(synapomorphies, synapomorphic) 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
(syncitia, syncytia, syncitium) 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 taxa
The taxa or named groups at the tips of the branches of a tree.
terrestrial
Pertaining to land - as opposed to the water (aquatic) or the air (aerial).
theca
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.
theront
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.
trichocyst
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.
trophic
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.
unicellular
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.
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