Glossary of terms
These definitions are taken from the Biology Online Dictionary (https://www.biology-online.org/dictionary/) unless otherwise stated.
Amoeba
Simple eukaryotic organisms that move in a characteristic crawling fashion. However, a comparison of the genetic content of the various amoebae shows that these organisms are not necessarily closely related (from Live Science, https://www.livescience.com).
Apomorphy
A trait of a clade or of species. An apomorphic character occurs “away” from the ancestral morphology, and therefore, may be referred to as the “derived trait” from the ancestral trait; it’s more like an “innovation” from the ancestral form. For example, a plant species that descended from a white-flower-bearing ancestor eventually became a red-flower-bearing species. The red-flower trait is an apomorphy, i.e., a trait that innovated from the ancestors and made that species “unique” from that found in its ancestor. That trait may also set it apart from other clades that descended from the same ancestor. Moreover, as noted in the online Biology Dictionary (https://biologydictionary.net/cladistics/), the difference between apomorphy and synapomorphy is that the derived characters of the latter condition are shared with the most recent common ancestor, while that is not necessarily the case with apomorphy.
Clade
A monophyletic group, i.e. a group of organisms (usually species) that are more closely related to each other than any other group, implying a shared most recent common ancestor.
Class
A taxonomic group comprised of organisms that share a common attribute. It is further divided into one or more orders.
Dentition
The character of a set of teeth especially with regard to their number, kind, and arrangement (from Merriam-Webster Dictionary online).
Dermal skeleton
Skeleton composed of dermal bone, which consists of bony structures (plates and scales) that develop in the skin (from University of California Museum of Paleontology, https://ucmp.berkeley.edu/vertebrates/vertmm.html)
Division
(1) A taxonomic rank at the level below Kingdom and above Class in biological classification of plants.
(2) A group of Classes with similar distinctive characteristics.
Embryology
The study of the embryo and its development from a single-celled zygote (fertilized ovum) to the establishment of form and shape (at which point, if it is an animal, it becomes a fetus).
Family
(1) A taxonomic rank in the classification of organisms between genus and order.
(2) A taxonomic group of one or more genera, especially sharing a common attribute.
Gametophyte
The sexual phase (or an individual representing the phase) in the alternation of generations - a phenomenon in which two distinct phases occur in the life history of the organism, each phase producing the other. The nonsexual phase is the sporophyte. (Encyclopaedia Britannica).
Ghost lineage
A line of descent that has left no traces in the fossil record (https://ucmp.berkeley.edu/taxa/verts/archosaurs/ghost_lineages.php).
Kingdom
A taxonomic rank that is composed of smaller groups called phyla (or divisions, in plants).
Lagerstätte
(plural: lagerstätten)
A fossil site exhibiting extraordinary preservation, commonly of soft body parts, and often faunal or floral diversity (http://www.fossilmuseum.net/fossilrecord/Lagerstatte.htm).
Larva
The early, immature form of any animal when more or less of a metamorphosis takes place, before the assumption of the mature shape.
Membrane
A thin layer of tissue covering a surface or lining a cavity, space or organ.
Metamorphosis
A change in the form and often habits of an animal after the embryonic stage during normal development.
Monophyletic
A group of organisms that are classified in the same taxon and share a most common recent ancestor. A monophyletic group includes all descendants of that most common recent ancestor (https://biologydictionary.net/).
Myomeres
Segments of trunk muscle (Encyclopædia Britannica)
Notochord
An elastic rod which extends through chordate organisms, providing rigid support. In the more derived chordates, the vertebrates, the notochord is replaced by the vertebral column, and becomes the cartilaginous substance between vertebrae (Biology Dictionary, https://biologydictionary.net/)
Nucleus
The large, membrane-bounded organelle that contains the genetic material, in the form of multiple linear DNA molecules organized into structures called chromosomes.
Order
A taxonomic rank used in classifying organisms, generally below the class, and comprised of families sharing a set of similar nature or character.
Paraphyletic
A group of organisms which contains a common ancestor and some, but not all, of the descendants (https://biologydictionary.net/).
Pharyngeal
Pertaining to the cavity at the back of the mouth.
Photosynthesis
The synthesis of complex organic material using carbon dioxide, water, inorganic salts, and light energy (from sunlight) captured by light-absorbing pigments, such as chlorophyll and other accessory pigments.
Phylogeny
The evolutionary development or history of a species or of a taxonomic group of organisms.
Phylogenetic tree
A tree diagram that shows the evolutionary histories and relationships of groups of organisms based on the phylogenies of different biological species.
Phylogenetic time tree
A phylogenetic tree that shows the geological age of its component nodes, branches and branch ends (or tips). However, the ages of nodes and branches of the time trees in this website are schematic rather than accurate in terms of millions of years.
Phylum
(plural: phyla or phylums)
(1) A taxonomic rank at the level below Kingdom and above Class in biological classification, especially of animals.
(2) A group of Classes with similar distinctive characteristics.
Polyphyletic
A taxonomic group is polyphyletic if its members have similar character states but the group does not contain the common ancestor of all the members.
Polytomy
A phylogenetic node that has more than two descendent lineages (University of California Museum of Paleontology web page “Phylogenetic pitchforks”, https://evolution.berkeley.edu/phylogenetic-systematics/reading-trees-a-quick-review/phylogenetic-pitchforks/).
Pseudopod
(plural: pseudopodia or pseudopods)
Temporary cytoplasmic projection of the cell membrane of certain unicellular protists, and is used in locomotion and/or in feeding by engulfing food.
Rhizome
A horizontal plant stem with shoots above and roots below serving as a reproductive structure.A type of storage organ in plants which situates itself in a horizontal fashion underground.
Sporangium
(plural: sporangia)
A spore case, within which asexual spores are produced.
Sporophyte
The nonsexual phase (or an individual representing the phase) in the alternation of generations - a phenomenon in which two distinct phases occur in the life history of the organism, each phase producing the other. The sexual phase is the gametophyte. (Encyclopaedia Britannica)
Squamation
Arrangement of scales on a fish.
(https://www.fishbase.se/glossary/Glossary)
Synapomorphy
A synapomorphy is a shared, derived character, common between an ancestor and its descendants. A character, or trait, is anything observable about the organism. It may be the size of the organism, the type of skin covering the organism has, or even things like eye color. A character may also be considered a specific sequence of DNA, which is how modern phylogenetic trees are constructed. (https://biologydictionary.net/)
Taxon
(plural: taxa)
(1) Any group or rank in a biological classification into which related organisms are classified.
(2) A taxonomic unit in the biological system of classification of organisms, for example: a phylum, order, family, genus, or species.
Time tree
A phylogenetic tree scaled to geological time (Hedges and Kumar, 2009).
Amoeba
Simple eukaryotic organisms that move in a characteristic crawling fashion. However, a comparison of the genetic content of the various amoebae shows that these organisms are not necessarily closely related (from Live Science, https://www.livescience.com).
Apomorphy
A trait of a clade or of species. An apomorphic character occurs “away” from the ancestral morphology, and therefore, may be referred to as the “derived trait” from the ancestral trait; it’s more like an “innovation” from the ancestral form. For example, a plant species that descended from a white-flower-bearing ancestor eventually became a red-flower-bearing species. The red-flower trait is an apomorphy, i.e., a trait that innovated from the ancestors and made that species “unique” from that found in its ancestor. That trait may also set it apart from other clades that descended from the same ancestor. Moreover, as noted in the online Biology Dictionary (https://biologydictionary.net/cladistics/), the difference between apomorphy and synapomorphy is that the derived characters of the latter condition are shared with the most recent common ancestor, while that is not necessarily the case with apomorphy.
Clade
A monophyletic group, i.e. a group of organisms (usually species) that are more closely related to each other than any other group, implying a shared most recent common ancestor.
Class
A taxonomic group comprised of organisms that share a common attribute. It is further divided into one or more orders.
Dentition
The character of a set of teeth especially with regard to their number, kind, and arrangement (from Merriam-Webster Dictionary online).
Dermal skeleton
Skeleton composed of dermal bone, which consists of bony structures (plates and scales) that develop in the skin (from University of California Museum of Paleontology, https://ucmp.berkeley.edu/vertebrates/vertmm.html)
Division
(1) A taxonomic rank at the level below Kingdom and above Class in biological classification of plants.
(2) A group of Classes with similar distinctive characteristics.
Embryology
The study of the embryo and its development from a single-celled zygote (fertilized ovum) to the establishment of form and shape (at which point, if it is an animal, it becomes a fetus).
Family
(1) A taxonomic rank in the classification of organisms between genus and order.
(2) A taxonomic group of one or more genera, especially sharing a common attribute.
Gametophyte
The sexual phase (or an individual representing the phase) in the alternation of generations - a phenomenon in which two distinct phases occur in the life history of the organism, each phase producing the other. The nonsexual phase is the sporophyte. (Encyclopaedia Britannica).
Ghost lineage
A line of descent that has left no traces in the fossil record (https://ucmp.berkeley.edu/taxa/verts/archosaurs/ghost_lineages.php).
Kingdom
A taxonomic rank that is composed of smaller groups called phyla (or divisions, in plants).
Lagerstätte
(plural: lagerstätten)
A fossil site exhibiting extraordinary preservation, commonly of soft body parts, and often faunal or floral diversity (http://www.fossilmuseum.net/fossilrecord/Lagerstatte.htm).
Larva
The early, immature form of any animal when more or less of a metamorphosis takes place, before the assumption of the mature shape.
Membrane
A thin layer of tissue covering a surface or lining a cavity, space or organ.
Metamorphosis
A change in the form and often habits of an animal after the embryonic stage during normal development.
Monophyletic
A group of organisms that are classified in the same taxon and share a most common recent ancestor. A monophyletic group includes all descendants of that most common recent ancestor (https://biologydictionary.net/).
Myomeres
Segments of trunk muscle (Encyclopædia Britannica)
Notochord
An elastic rod which extends through chordate organisms, providing rigid support. In the more derived chordates, the vertebrates, the notochord is replaced by the vertebral column, and becomes the cartilaginous substance between vertebrae (Biology Dictionary, https://biologydictionary.net/)
Nucleus
The large, membrane-bounded organelle that contains the genetic material, in the form of multiple linear DNA molecules organized into structures called chromosomes.
Order
A taxonomic rank used in classifying organisms, generally below the class, and comprised of families sharing a set of similar nature or character.
Paraphyletic
A group of organisms which contains a common ancestor and some, but not all, of the descendants (https://biologydictionary.net/).
Pharyngeal
Pertaining to the cavity at the back of the mouth.
Photosynthesis
The synthesis of complex organic material using carbon dioxide, water, inorganic salts, and light energy (from sunlight) captured by light-absorbing pigments, such as chlorophyll and other accessory pigments.
Phylogeny
The evolutionary development or history of a species or of a taxonomic group of organisms.
Phylogenetic tree
A tree diagram that shows the evolutionary histories and relationships of groups of organisms based on the phylogenies of different biological species.
Phylogenetic time tree
A phylogenetic tree that shows the geological age of its component nodes, branches and branch ends (or tips). However, the ages of nodes and branches of the time trees in this website are schematic rather than accurate in terms of millions of years.
Phylum
(plural: phyla or phylums)
(1) A taxonomic rank at the level below Kingdom and above Class in biological classification, especially of animals.
(2) A group of Classes with similar distinctive characteristics.
Polyphyletic
A taxonomic group is polyphyletic if its members have similar character states but the group does not contain the common ancestor of all the members.
Polytomy
A phylogenetic node that has more than two descendent lineages (University of California Museum of Paleontology web page “Phylogenetic pitchforks”, https://evolution.berkeley.edu/phylogenetic-systematics/reading-trees-a-quick-review/phylogenetic-pitchforks/).
Pseudopod
(plural: pseudopodia or pseudopods)
Temporary cytoplasmic projection of the cell membrane of certain unicellular protists, and is used in locomotion and/or in feeding by engulfing food.
Rhizome
A horizontal plant stem with shoots above and roots below serving as a reproductive structure.A type of storage organ in plants which situates itself in a horizontal fashion underground.
Sporangium
(plural: sporangia)
A spore case, within which asexual spores are produced.
Sporophyte
The nonsexual phase (or an individual representing the phase) in the alternation of generations - a phenomenon in which two distinct phases occur in the life history of the organism, each phase producing the other. The sexual phase is the gametophyte. (Encyclopaedia Britannica)
Squamation
Arrangement of scales on a fish.
(https://www.fishbase.se/glossary/Glossary)
Synapomorphy
A synapomorphy is a shared, derived character, common between an ancestor and its descendants. A character, or trait, is anything observable about the organism. It may be the size of the organism, the type of skin covering the organism has, or even things like eye color. A character may also be considered a specific sequence of DNA, which is how modern phylogenetic trees are constructed. (https://biologydictionary.net/)
Taxon
(plural: taxa)
(1) Any group or rank in a biological classification into which related organisms are classified.
(2) A taxonomic unit in the biological system of classification of organisms, for example: a phylum, order, family, genus, or species.
Time tree
A phylogenetic tree scaled to geological time (Hedges and Kumar, 2009).