The Upright Ape: A New Origin of the Species

by Aaron G. Filler, MD, PhD


- A -

allele – version of a gene. Animal genomes have two copies of each gene – one from each parent. The two copies may be the same or may produce alternate versions of what is controlled or produced by that gene.

allometry – the alteration of the size relationships of various body parts that is related to the overall total size of the organism – e.g. a mouse has very small legs relative to body size when compared to an elephant.

amino acid – the component molecular units that are assembled into chains to make proteins.

amniote – an animal group that includes all  reptiles, birds and mammals defined by a shared aspect of the embryonic amniotic membrane. This allows the eggs to be laid away from water. The same membrane is found in mammals.

amphibian – an animal group that includes the early land vertebrates (tetrapods), but does not include the amniotes. It is a “paraphyletic” term. Modern members include the frogs and caecilians.

amphioxus – a primitive or simple vertebrate animal.

analogous – a feature seen in two different species that is similar in appearance but not truly identical on the basis of genetic origin.

Antennapedia – An allele that affects the segmental determination of the antenna of a fruit fly. A mutated version is known that causes legs to appear in place of the antennae because the identity of the head segment is detected as the identity of an abdominal segment in the homeotic assembly sequence of the animal’s embryo (see figure 1-3).

Anthropoidea – a group at the SuperFamily level that includes monkeys, apes and humans (see figure 10-4).

apomorphy – a new or derived version of a character state.

appendicular – relating to arms or legs

Archaea – a group of organisms not included in the bacteria, plants, fungi or animals.

Archosauria – a group of animals that includes alligators, dinosaurs and birds.

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Bilateria – a group of animals with bilateral symmetry that includes many of the invertebrate phyla such as insects as well as the vertebrates.

body plan – the basic layout of the body that is a distinctive aspect of  a group of animals.

Book of the Dead – also called the Book of Going Forth by Day. A collection of funerary texts and spells that were often placed with an Egyptian mummy at the time of burial. The Papyrus of Ani is a particularly elegant and well preserved version.

brachiation – locomotion accomplished by overhead arm swinging. It is the main method of locomotion in hylobatid apes and is used occasionally by other hominoids (apes and humans) and in a group of New World Monkeys called the atelines (spider monkey Ateles) where it developed separately as an evolutionary parallel convergence or analogous trait (see figure 9-3).

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Cambrian Explosion – A rapid increase in the number of animal body plans, phyla, classes, and orders that took place in the early Cambrian era between 540 and 490 million years ago.

catalytic site – The portion of an enzyme protein that actually carries out the expedited chemical reaction that is the enzyme’s main function

catarrhine – A group of primates that includes the old world monkeys and the hominoid apes and humans. The sister group is the platyrrhine new world monkeys (see figure 10-4).

cation – An element dissolved in water can attract or lose electrons giving it a positive or negative charge when it is dissolved in water. When the electrons are lost, the atom becomes a positively charged ion. When two are lost it is a divalent cation. When three are lost it becomes a trivalent cation. Electrons are organized in series of orbital shells around the positively charged nucleus. In transition metals, the outer "valence shell" is occupied by two "spin paired" electrons (4s shell) that are relatively loosely bound and which can be lost - particularly when the metal is "solvated" (dissolved in water). Alkali earth metals such as magnesium can lose their two (3s) valence shell electrons and transition metals such as manganese tend to loose two electrons from their 4s shell although it is their d-shells that are incomplete. Lanthanoids, scandium and yttrium lose three electrons. The electrons of the valence shell are more loosely held by the atom because of their distance from the protons in the nucleus and because the electrons in the inner shells provide some electrostatic shielding from the positive attraction of the nuclear protons.

caudal – Towards the tail.

ceboids – A group of primates including the new world monkeys (platyrrhines).

centromere – The point of connection between the two sister chromatids that carry the two duplicated copies of each chromosome after replication just before cell division. It is also the point of attachment of the spindle fibers which will pull the chromatids apart towards appropriate ends of the dividing cell. 

centrum – The major portion of the vertebral body – the various processes (extensions) and arch components are attached to the centrum and the discs are between the centra.

Cephalopods – A group of animals in the Mollusks that includes the squid and octopus.

cercopithecoid – A group of primates termed the Old World Monkeys (see figure 10-4).

Cerium – An element in the lanthanoid group.

cervical – Relating to the neck.

Cetacea – A group of animals that includes the whales and dolphins

Cetartiodactyla – A group animals reflecting the emergence of the Cetacea the Hippopotamus group. This term includes all the Cetacea and all the Artiodactyla – ungulates animals with split hooves (antelope, cattle, camels).

character – A word used in systematic biology and evolution to describe a genetically determined feature of an organism.

character polarity – When several different versions of a feature is observed in various species, it is helpful to try to determine which is the older or primitive version and which are the more modified or derived versions that evolved later by further modification of the original character. This determination will identify the polarity – which version came first, which came last.

chelation – The process whereby some types of chemical molecules can attach to or bind metal cations.

chemoautotrophic – The ability of some organisms to generate glucose from its chemical constituents using chemical or other physical energy other than light. These are all either Bacteria or Archaea.

chloroplast – The component organelles inside each plant cell that capture the energy of sunlight to catalyze a reaction that produces glucose from carbon dioxide gas and water - photosynthesis.

Chokras – Description of  levels of consciousness and existence within the human body and soul that derive from the ancient Hindu Vedic literature. They bear some analogy with the series of segments in the body.

chordata – The phylum that includes the deuterostome groups such as vertebrates who all share a structure called the notochord - a long linear structure running the length of the body - at some point in their embryological or adult anatomy.

chromatids – The two identical chromosome copies produced by DNA replication just prior to cell division in mitosis and the first round of division in meiosis. They are joined together at the centromere resulting in the “X” shaped appearance of most chromosomes. (This is a different issue than the X & Y sex chromosomes) (see figure 4-2).

chromatin – The protein and nucleic acid material that includes the packaged and compacted chromosomes in the nucleus of the cell

chromosomal speciation – A process of separation or origination of  a new species resulting from a reorganization of the chromosomes (see figure 4-1).

Cilia – Small hairlike projections that line the surface of many types of cells and organisms that have a motile or movement capability.

cinefluoroscopy – Motion picture X-ray obtained by filming the fluoroscopy exposure screen while it is continuously illuminated by X-rays passed through a moving object of interest (also cine-X-ray).

cis-acting – Regulatory genes in place along a strand of DNA that encodes a genetic instruction

clade – Any natural group of organisms that share a common ancestor

Cladist – A specialist in systematic classification of organisms that adheres to the principles established by Willi Hennig in Phylogenetic Systematics (see figure 5-3).

Cladogram -  A branching tree drawing that shows the relationships among organisms.

cloven – The split hoof that represents structures homologous to two finger nails is described as a cloven hoof. This term is applied to artiodactyls including goats, cows, antelopes, and camels.

coccygeal – Pertaining to the vestigial tail (coccyx) in hominoid primates. Homologous to the first few caudal or tail vertebrae in other tetrapod vertebrates.

Coelacanth – A living species of fish that is one of the few surviving members of the sarcopterygian fish group that is most closely related to the land tetrapods (amphibians, reptiles, mammals, birds)

cold-blooded – Technically poikilothermic – animals that do not maintain an elevated body temperature (homeothermic). The homeothermic animals include birds and mammals and may include dinosaurs

combustion – The consumption of oxygen in burning.

conservative – In biological usage – this refers to characters or organisms that demonstrate relatively little external anatomical change over time.

convergence – The appearance of similar appearing features in two species where the features arose and evolved independently along separate line to reach similar endpoints.

Coptic – An Egyptian language in the Semitic language group.

cranial – To do with the head.

cranial mesoderm – The three main tissue forming layers of the embryo are the ectoderm (skin and nervous system), endoderm (gut lining) and mesoderm. The mesoderm participates in the formation of muscles and bones among other tissues. The mesoderm participating in formation of the head in the embryo is described as the cranial mesoderm.

cranial segments – Separate modules with identified homeotic identities that contribute to the embryonic development of the head.

cranium - Skull

Cretaceous – The third major period of the Mesozoic era from 144 to 66 million years ago. At the start of the Cretaceous, dinosaurs were abundant and mammals scarce and tiny. At the close of the Cretaceous, dinosaurs became extinct and birds and mammals had begun their major diversifications.

crocodiles – Amniote animals can be described as the reptiles who are most closely related to the dinosaurs and birds (the archosaurian group).

crustaceans – A phylum of protostome (invertebrate) animals that includes lobsters and shrimp and that are related to the arthropod insects and spiders.

cyanobacterium – A group of blue-green bacteria capable of capturing sunlight to help provide energy to form glucose (photosynthesis). They are sometimes called blue green algae but are not technically algae (which are eukaryotic single and multi-cellular plants).

cynodonts – A group of synapsid reptiles (amniotes) close to the ancestry of mammals.

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Darwinian threshold – A time point in the early evolution of each major kingdom of life at which “vertical” transmission of genetic information from parent to offspring, becomes more important than “horizontal” gene transfer (HGT) wherein genes are transferred from one kind of organism to another by mechanisms such as inadvertent viral incorporation of genes and subsequent recombination.

dental apes – A group of fossil ape species that are identified as hominoids (apes) primarily because of the features of their teeth.

deoxyribonucleic acid – The molecular substance of the polymer that stores genetic information (DNA).

derived morphology – A version of an anatomic feature of a species that is modified or changed relative to a similar feature in an ancestral species.

Dermoptera – Bats.

deuterostome – A group of animals (including the vertebrates) that share a similar pattern of embryonic assembly in which the blastopore of the embryo forms the anus as opposed to forming the mouth as it does in protostomes (invertebrates) (see figure 7-1).

development – Used in biology to describe the progress of growth, specialization and morphogenesis whereby the product of  egg and sperm  (the embryo) gradually assembles itself into a fully formed adult animal.

Devonian – A time period in the Paleozoic era extending from 408 to 360 million years ago. During this time, the earliest tetrapods emerged on the land.

diagonograde – The posture employed by chimpanzees and gorillas when they use the extended arm, flexed leg posture of knuckle-walking and related gaits. The trunk is held at about 45 degrees relative to the ground as opposed to parallel with the ground (pronograde) or vertical (orthograde) (see figure 10-1B).

diaphragm – A large flat muscle that divides the chest from the abdomen in mammals and which helps expand the lungs for breathing in when it contracts

diapsids – A group of amniotes defined by features of the skull (two openings) which includes lizards, snakes, archosaurs, and birds. This excludes the synapsid reptiles (one opening) and their mammalian subgroup as well as the anapsid reptiles (no opening) made up by the turtles. Both diapsids and anapsids can be included in the Sauropsida which is the sister group to the Synapsida.

diarthrum – The join surface on the lateral aspect of the arch (or thoracic transverse process) of a vertebra that articulates with (contacts) the more dorsal of the two heads on the ribs of most tetrapods – the tuberculum of the rib. The more ventral of the two heads on each rib (the capitulum) articulates with the pararthrum (see figure 8-6).

differentiation – The process during embryogenesis by which, cell types become progressively more specialized.

digitigrade – Standing or walking on the fingers as opposed to the palms (palmigrade) or the fingernails (unguligrade).

digits – Used anatomically to refer to fingers and toes.

dinosaur – A name proposed by Sir Richard Owen to describe the often large and often bipedal archosaurs of the Mesozoic period. Technically these are diapsid non-bird, non-crocodilian archosauria.  They may also be described in terms of their two major subgroups the Ornithischia and Saurischia.

divalent – A chemical or physical term referring to cationic versions of dissolved elements that have two quantums of electronic charge

divergence time – The point in geologic time at which two lineages separated from each other.

diversification – The generation of additional species within a higher group

Djed cross – A symbol of the spine of Osiris involving a vertical and four cross bars (see figure 3-2).

DNA replication – The process of copying DNA in preparation for a cell division event.

DNA sequence – The spelling out of the information content of DNA as a patter of the four types of DNA monomers  - thymine, adenine, guanine, cytosine.

DNA-binding – Proteins or nucleoprotein complexes that adhere to a DNA molecule.

Domains of life – The major groups of living organisms – Bacteria, Animals, Plants, Fungi and Archaea

dominant allele- When two different allelic versions of a gene are present, the resultant phenotype or observable product be of the type of specified by the dominant allele whether or not a recessive version of the allele is present.

dorsally – towards the back of an animal

dorso-ventral axis – A conceptual direction line from the back to the front of the organism.

dorso-ventral patterning -  In the course of embryologic development, the assignment and positioning of characters along the dorso-ventral axis.

Drosophila – The fruit fly. It is widely studied in genetics because it is a model organism with very rapid generation time with many known mutations.

Dryopithecus – A genus of hominoids or apes from the Miocene.

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Echinodermata – Starfish. These are in the deuterostome group along with the vertebrates, but do not have a notochord.

ectoderm – One of three basic tissue types in the early embryo. It gives rise to the skin and nervous system among other tissues.

Ediacran fauna – An array of extinct organisms present in the late Pre-Cambrian and Early Cambrian eras which disappeared at  the time that the Bilaterians were undergoing the rapid diversification called the Cambrian Explosion.

Electromyography – A method of studying muscle function that relies on electrodes placed over or inserted into muscles. These are used to detect and record the electrophysiologic process of muscle activation that occurs when an animal initiates activity of each individual muscle

electron – A fundamental component of matter that contains a negative electric charge.

electrophoretic gel separation – A process of separating large biological molecules such as proteins and DNA fragments based on their size and charge. A mixture is applied to one end of a long thin gel – often made of polymerized polyacrylamide – and an electric field is applied. The molecules are dragged from one end of the gel towards the other end by the electric field attraction, but smaller molecules travel more rapidly through the gel. When the electric current is turned off, the mixture of molecules is now separated along the gel according to size (see figure 6-3B).

embolomeres – A group of earl tetrapod amphibians (anthracosaurs) found in the Carboniferous (360 to 300 mya) and Permian (300 to 250 mya) periods of the Paleozoic (540 to 250 mya) era.

embryogenesis – The process of progression from a fertilized egg to a fully differentiated and patterned embryo.

endoskeleton – The skeleton of vertebrates is typically internal in location (endo) as opposed to the skeleton of many invertebrates which is external (exoskeleton).

endosymbiosis – Two different types of organism whose lives are interdependent are symbiotic. In endosymbiosis, one organism lives inside the cells of the other organism.

entomologist – A specialist in insect biology.

enzyme – A protein that acts to accelerate a chemical reaction. Other types of proteins may be structural or regulatory.

epaxial muscles – The muscles of the spine that are dorsal to the dorso-ventral septum of the body. This includes the iliocostalis, the longissimus and the transversospinalis muscles.

Euarchontoglira – A superorder of placental mammals that includes primates, rodents and rabbits.

Eukarya – A group of organisms that that have a nucleus in each cell. This excludes the bacteria which are prokaryotes and have their DNA in the main cytoplasm of the organism rather than packaged into the nucleus.

eumycote – The main group of fungi. These organisms share the use of motile sperm with the animals but are heterotrophs like animals (they must ingest their food). They are sessile (tend to attach to one location and never move) and they have cell walls that are analogous to those plant cells but absent in animal cells.

eutherians – A group of mammals arising in the Late  Cretaceous whose young develop in the uterus, fed by a placenta, until birth as an independent motile organism. Other existing mammals are either metatherians (marsupials) who are born very early and attach to the mothers teats in a pouch rather then employing a placenta, or monotremes (Prototheria) whose young hatch from externally deposited eggs.

Evo-Devo – A category of evolutionary thought that places particular importance on embryological mechanisms in the understanding of evolutionary change (also Evolutionary Developmental Biology).

exoskeleton – The external skeleton – typically made of a hard material called chitin that is related to starch – that is found in many invertebrate (protostome) phyla.

extant – Living or current species.

- F -

facets – Joints between the dorsal or arch structures of adjoining vertebrae.

field homology – A type of similarity among structures that relates to their position in embryological morphogenetic fields and gradients rather than their original genetic composition.

flagellum – A type of mobile external projection found in some single celled organisms and in sperm whose whiplike motion causes forward motion.

- G -

gadolinium – An element in the lanthanoid series of the periodic table.

gamete – A reproductive cell that is the result of a type of cell division called meiosis. It has only a single copy of the organism’s genome and that copy is a mixture of the gene set obtained from that organisms mother and father.

gamma ray – Electromagnetic radiation similar to light, but with higher energy. These rays can penetrate solid tissue and cause genetic mutations when they cause damage to DNA.

ganglia – Collections of connecting nerve cells outside of the main central nervous system (brain and spinal cord)

gene duplication – The process whereby the genome of an organisms begins to carry two copies of a given gene.

gene expression – The effect that results when a gene is transcribed into the gene product that the gene encodes – such as enzyme.

gene frequency – The relative rate of occurrence of a given gene or allele of a gene within a population of species members considered relative to the rate of occurrence of a different allele or of individuals that do not have any version of that gene.

gene pool – The total collection of all the genes in and all their alleles in a given interbreeding population – often in an entire species.

genome – The total set of all of the DNA that makes up the full instruction set of a species.  This may include DNA that does not produce any functioning product.

germ line – A set of cells destined to be organized into eggs or sperm.

gibbon – A small southeast Asian ape that walks bipedally on the ground and arm swings (brachiates) in the trees. Along with the siamang (Symphalangus) the gibbons (Hylobates) make up the Hylobatid family of hominoids. They are hominiforms because they are likely to be descendant from the same group as Morotopithecus along with humans and the other living apes (see figure 9-3).

gill – A structure used by fish to extract oxygen from water. The water is generally flowed into the animals mouth then forced back out through the gills. Gas exchange takes place along the walls of the gills.

glaciation – The process of formation and movement of glaciers.

- H -

Hennigian – Description of a method of systematics (classification of organisms) based on the principals outlined by Willi Hennig in Phylogenetic Systematics – also called cladistics.

heritable – A change in the organisms traits – at the level of the genes in the germ line  - that can be passed along to future generations.

hexapods – A group of invertebrate (protostome) animals that includes the insects.

higher primates -  General term for the Anthropoid primates – New World Monkeys, Old World Monkeys, and hominoids (apes and humans) but excluding prosimians (lemurs and galagos) (see figure 10-4).

HOM – High Order Module – this is a component of an organism – at some stage in its development - that includes a full set of interacting tissues and organs and is typified by the somite or insect segment.

homeobox – (also homeo box) A region found in a variety of genes that marks them as playing a role in differentiating the various segments of an organism relative to each other based on their position along the organisms main cranial-caudal body axis. (Also homeodomain).

homeodomain - A region of proteins that are coded by the homeobox gene sequence. This region is involved in binding to the DNA of transcription promoters that play major roles in morphogenesis.

homeotic evolution – Changes in the anatomy or morphogenesis of an organism based on different qualities of its component segments and their position along the main cranial-caudal body axis.

homeotic genes – Genes that affect the identification and specialization of the various body segments based on their position along the main cranial-caudal body axis (see figure 7-5).

hominid – The family of hominoids that includes the genus Australopithecus and the genus Homo. The term is used in various ways by various authors and may include a number of other hominoid genera and subfamilies depending upon the source.

hominiform – A natural group of hominoids including humans and all existing apes that share a major homeotic change in the spine that appears to underlie upright posture in the group. The earliest known member is Morotopithecus from 21.6 million years ago.

hominiformid – A family of hominoids equivalent to the cladistic term “hominiform”. It excludes fossil hominoid groups that do not show evidence of the transformed spinal anatomy such as the proconsulid family of hominoids.

hominin – A subfamily of hominoids including Australopithecus and Homo as well as various other upright bipedal species such as Sahelanthropus, Ardipithecus, and Paranthropus. It is applied in various ways by various authors.

hominoid – A group of catarrhine primates that excludes the old world monkeys (cercopithecoids). They share several characteristics such as a Y-5 dental pattern of molar cusps.

HomoA genus of upright bipedal hominoids that includes Homo habilis, Homo erectus, Homo ergaster, and Homo sapiens.

Homo erectus – A species of the genus Homo that is known from 2.5 to 0.4 mya. The body form was very similar to modern humans, but the brain size was typically about 75% of the average modern human.

Homo habilis – The earliest species assigned to the genus Homo – dating from 2.5 to 1.8 million years ago. They are distinguished from Australopithecus species by their frequent production of shaped stone tools. Brain size was about 45% of what is typical in modern humans.

homologous – A description of a feature in two species that has identical origin and genetic basis.

homologous chromosome – In a “diploid” organism (such as most animals) there are two copies of the entire genome. The homologous chromosomes are the two similar chromosomes – one originating with the father and one originating with the mother -  that may be paired with each other. The X and Y chromosomes are homologous but not identical (see figure 4-2).

homologous protein-coding sequence – A portion of a genes that appears to have the same origin as a similar portion in a different gene.

homology – Various concepts of similarity of features among organisms have been developed to explain the biological phenomenon of genetically related parts. The oldest and original version was proposed by Sir Richard Owen relative to the conceptual archetype. Most recently, homology has been considered in terms of patterns of homeotic and other morphogenetic genes.

homoplasy – The development of a similar character state in two species by independent, non-homologous processes and histories. Also described as the result of parallel or convergent evolution. The structure may be analogous, but homoplasy also applies when a character becomes absent in two species independently.

hopeful monster – The description of Richard Goldschmidt’s concept of the abrupt emergence of an abnormal individual that may herald the origin of  a new kind of animal.

horizontal gene transfer (HGT) – A process, often involving viruses, whereby a gene can be transmitted from one organism to another without being passes “vertically” in a lineage from parent to offspring. This process dominated evolution before the emergence of vertical lineages occurred at various “Darwinian Threshold” points in various types of animals.

Hox gene – A gene containing a homeobox region. These genes are typically involved in controlling aspects of morphogenesis that involve assigning identities to various segment along the cranio-caudal body axis. Genes which include the homeobox and which also occur in the highly structured Hox cluster portion of the genome are termed Hox genes.

Humanian model – New term for a model of hominoid evolution in which upright bipedal hominiforms that can be termed humans are considered to have been present since the time of Morotopithecus 21.6 million years ago. This is contrasted with the Hylobatian model (that sees the hylobatid gibbons and siamangs as models for an ancestor) and the Troglodytian model (that sees humans emerging from a knuckle walking ancestor similar to a chimpanzee).

Hunterian Lecture -  A series of lectures given annually at the Royal College of Surgeons of England in honor of the bequest of the Hunterian anatomical collection to the RCS in the late 1790s. These lectures have been used by Sir Richard Owen, Sir William Flower, Thomas Henry Huxley, and Sir Arthur Keith to present major new concepts in the evolutionary theory and human origins.

hybrid – A biological use of this term is to refer to the progeny of two different strains or two different but closely related species.

Hylobatian model – A model of human evolution proposed by Sir Arthur Keith in the early 20th century, that emphasized the importance of the upright adaptations of the hylobatid apes (gibbons and siamangs) for understanding human origins.

hyoid – A small bone in the throat of land vertebrates that is homologous to one of the gill arches in fish. Various efforts to understand the homology of this bone have played a major role in several rounds of development of evolutionary theory over the past 220 years.

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intercentrum – A part of the vertebral body (centrum) that has gradually been reduced in size relative to the pleurocentrum and which is now absent in nearly all amniote species.

intercostal muscles – Muscles placed between the ribs that play a role in breathing.

intermaxillary – A small bone in the palate whose presence in humans had been missed by most 18th century anatomists. Goethe’s demonstration of its presence in humans supported his claim that humans fit into the general pattern of animals in nature.

intertransverse – Ligaments or muscles extending between the lumbar transverse processes in mammals

invertebrates – A description of Metazoans (multi-cellular animals) that are not in the Vertebrate group. This general category has been replaced by embryological description “protostomes” in many settings.

Isis – A god in Egyptian religion who was the wife and sister of Osiris and who bore a son, Horus, through immaculate conception.

- J -

- K -

knuckle-walking – A description of one method of hand posture during diagonograde locomotion by chimpanzees and gorillas (see figure 10-1).

- L -

lamina – The dorsal arch of the vertebra that stretches from left to right, stands upon the pedicles, and serves as the roof  over the spinal canal that contains the spinal cord and spinal nerves.

laminapophysis – A vertebral process found in mammals that extends from the lamina. It is subject to a wide variety of morphologic transformations.

lordosis – Curvature of the cervical and lumbar spine in humans

LTP – Lumbar transverse process – an extension from the lateral aspect of the vertebra in therian mammals that is derived from various different underlying vertebral components in different mammalian lineages. It structure is greatly transformed in hominiform primates.

LUCA – Last Universal Common Ancestor – an organism existing over a billion years ago from which all types of existing life are descended.

Lucy – A specimen of Australopithecus afarensis discovered by a team led by Donald Johanson.

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macroevolution – Patterns of evolution that affect higher groups or large scale trends among organisms.

magma – Molten rock from the mantle of the earth that may emerge through the crust as volcanoes or as new crust formation at mid-oceanic ridges.

magnesium –  A soft metallic element that is required in its divalent cation form as a cofactor for normal function of various enzymes including the polymerase enzymes that replicate DNA.

Magnetic Resonance Neurography -  A new method of magnetic resonance imaging that provided detailed images of the nerves (see figure 10-5).

Mammalia – A group of amniotes that emerge from among the synapsid reptiles. They share a variety of feature including the feeding of their young via milk secreted from mammary glands.

mammal-like reptile – A group of reptiles, also called the synapsids, out of which mammals emerged. The term is often used specifically for synapsid reptiles groups closest to the earliest mammals.

marsupial – A group of mammals (Metatheria) whose young are born early and grow attached to the mammary teats in a pouch rather than being hatched from an egg as in monotreme mammals (Prototheria) or being subject to extended growth fed by the placenta in eutherian mammals.

meiosis – The process of cell division that results in the formation of gametes that have a single set of genetic information as opposed to the double (diploid) set present in other somatic cells in animals (see figure 4-2).

Mendelian genetics – An approach to heredity that relied on the identification of traits as discrete items that seemed to sort and mix according to mathematical rules. It is now knows that these Mendelian traits are in fact the genes arrayed along the chromosome.

meristic variation – Alteration in the number of body segments that involved adding or removing segments rather than changing the identity or outward form of existing segments (homeotic variation).

mesenchyme – An embryonic tissue formed from the mesoderm that gives rise to various tissues including the muscles.

Mesozoic – An era of geologic time between 245 and 66 million years ago that was the major period of dinosaur dominance. It is divided into Triassic (245 to 208 mya), Jurassic (208 to 144 mya) and Cretaceous (144 to 66 mya) periods (see Timeline).

mesozoic mammals – An array of mammalian groups including the direct ancestors of the existing Prototheria (monotremes) and the lineages out which the therians (eutherian and metatheria) arose. Also included are multituberculates, triconodonts, and symmetrodonts. The closest group to the therians are the Tribosphenida and this group is sometimes used to include therian mammals along with some extinct Cretaceous groups.

metacarpo-phalangeal joint – The joint between the metacarpals – which make up the palm and back of the hand – and the first or proximal phalange of the finger.

metameric pattern – The organization of a larger entity out of smaller segments.

metaphysical – Rooted in philosophy rather than in objective observation.

metatherians – Marsupial mammals.

Metazoa – Multi-cellular animals – from sponges to humans.

meteoroid – A relatively small celestial object – from 0.1 mm to 10 meters in diameter. A larger object in space that is smaller than a planet  - whether or not it orbits a star – is an asteroid.  Once a meteoroid enters the atmosphere and causes a visible streak of light in the sky – it is a meteor. If it survives the passage through the atmosphere, the portion that hits the ground is a meteorite.

midcarpal joints – Joints among the multiple bones of the wrist.

Miocene – Geologic epoch extending from 24 million years ago to 5 million years ago (see Timeline).

mitochondria – An organelle within the cell that provides the capability of generating energy by consuming oxygen. It has its own genome and is generally considered to have arisen as an endosymbiont bacteria living within an early eukaryotic cell.

mitochondrial genomes – The genes of a mitochondrion. They evolve more rapidly than the nuclear genome and have maternal transmission – all of ones mitochondria come from the egg of the mother with none from the sperm. They may be used for studying evolutionary relationships along with nuclear genes.

mitosis – The process whereby a somatic cell divides into two daughter cells (see figure 4-2).

Modern Synthesis – The expansion and update of Darwinian evolutionary theory in the 1940’s to include population genetics.

modularity – In biology, the consideration of anatomy, genetics, or biochemistry of organisms from the point of view of assembling together smaller working units that may be complex working systems themselves.

molecular biology – The area of biology dealing primarily with nucleic acids (DNA/RNA).

molecular clock – A basis for assessing the divergence times of lineages by comparing the amount of differences in their DNA. The underlying assumption is a more or less steady accumulation of DNA changes over time. The clock is generally calibrated by firmly placed fossils. It is a complex measure because different types of genes and non-gene DNA in different groups of organisms appear to accumulate changes at varying rates.

molecular cloning – Producing multiple identical versions of a molecule or an entire organism by a process that commences with duplicating the responsible genes.

monomer – A single component of a multi-segment or polymeric entity.

monophyletic – A natural group of animals that share a common ancestral species (see figure 5-3).

monotremes – A group of mammals (Prototheria) that diverged from other modern mammalian groups early in the age of dinosaurs. Young are born from externally deposited eggs. Examples are the duckbilled platypus and echidna.

Moroto – A volcano in Uganda near the edge of the East African Rift Valley.

Morotopithecus bishopi – A Miocene hominoid known from fossils whose vertebrae demonstrate numerous similarities to those of modern humans. It may be close to the founding species of the upright hominiform group of hominoid primates. Other Miocene hominoids that do not share the human-like vertebral features are considered to be in the proconsulid group. The name reflects the Moroto volcano site where it was found and the name of the discoverer William Bishop. The specimen has been variously attributed to Proconsul major or Dryopithecus major in the past. Other genera names found at the same time and general locale include Afropithecus and Ugandapithecus.

morphogenetic – Involved in the direction of assembly of the shape and structure of the progressing embryo.

morphological – Related to the observable shape or anatomy of an organism.

morphological novelties – The appearance of new anatomical structures not seen in ancestral species, also – neomorphs.

morphospace – The conceptual array of all possible morphologies. Existing organisms occur within a very limited area of the potential total morphospace – e.g. we don’t have fish with eyes along their tails, or mammalian species with seven legs, etc.

multi-cellular – Organisms composed of multiple cells that have genetically determined roles relative to each other.

mummies – Bodies of Egyptian people (or animals) from the historical dynasties that were preserved by a process that included wrapping in linens, a chemical embalming process, and typically a burial in a coffin, sarcophagus, or case.

mutation – A change in the DNA of an organism that can be inherited because it is present in the germ cells.

mutationist – A biologist who believes that mutations can occur in patterns, specific locations and sequences that can provide direction to evolutionary change. Alternately, we can consider that mutations simply provide a continual and directionless array of variations with directed evolution being driven solely by natural selection.

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Natural philosophy – Applied primarily to a late 18th and early 19th century German school of thought that applied philosophical considerations to the understanding of biology (Naturphilosophie).

natural selection – The effect of survival of the fittest in causing individual species members who have a more effective mix of inheritable genetic variations to reproduce more successfully than other species members. The demands of survival in nature will select the genetic variants within a species population that are more likely to be passed on to descendants. This is a key innovative component of Charles Darwin’s theory of evolution.

Neanderthal – A sub-species of Homo sapiens (H. sapiens neandertalensis) that is replaced by modern Homo sapiens sub-species (H. sapiens sapiens) during the past 100,000 years. Some specialists consider neandertal to be a distinct species rather than a sub-species. Brain size is slightly larger than modern humans.

nematodes – A phylum of worms that are related to the insect group and other invertebrate phyla that shed their exoskeletons periodically.

neodymium – An element in the lanthanoid series of the periodic table.

neomorphic – A newly elaborated anatomical (morphological) structure.

NeoProterozoic – The last portion of the Precambrian geologic supereon and of the Proterozoic eon. Extending from 1 billion years ago to 540 million years ago. The period of time following the NeoProterozoic is the Phanerozoic and this extends to current time. The Proterozoic eon extends from 2.5 billion years ago to 540 million years ago. It is preceded by the Archaean eon (3.8 billion years ago to 2.4 billion years ago) and by the Hadean eon (4.6 billion years ago the 3.8 billion years ago) (see Timeline).

nerve – A modified type of cell that typically has a single long extension called an axon. An electrical depolarization signal can travel from the cell body to the axon terminus resulting in directional flow of information. At the terminus, either electrical or chemical communication allow the nerve to trigger activation in another cell (possibly another nerve cell) that it contacts.

nervous system – The total collection of nerves that exist in an organism.

neural crest – A series of cell clumps along the margin of the forming spinal cord that give rise to spinal ganglia and other tissues in the process of embryogenesis in vertebrates.

Neurography – A magnetic resonance imaging technique that provides a detailed view of the nerves in a living organism (see figure 10-5).

NHP SRE’s - Monomers in bilaterian organisms can be described from the point of view of their genetic characteristics as Notch generated, Hox determined, and Pax organized serially repeating elements.  All of insect segments, vertebrate somites and vertebrae are therefore “NHP SRE’s.” Notch is a gene involved in causing the splitting of tissue into separated segments. Hox genes relate to the segmental identities based on position along the cranial-caudal body axis and Pax genes are involved in organization along the dorso-ventral axis of the body.

Nodal – A gene whose product relate to formation of the neural tube, and which is implicated in right left axis determination in vertebrates.

non-bird – Cladistic terminology for animal groups requires that names be “holophyletic and monophyletic” – that is they must describe all the members of a group with no excludes sub-group of the descendants and all must have a shared single ancestor. The term Dinosaur fails these conditions. It is a monophyletic group but it excludes the descendant group we call birds. We can refer to Dinosaurs as non-bird, non-crocodilian,  archosaurs.

non-Darwinian Evolution – The word “Evolution” – at its core – implies descent with modification attended by a repetitive process of new species formation, but Darwinian evolution requires the modifications to emerge gradually through the direction provided by the impact of natural selection on competing individuals in a species with randomly varying small changes in their genes. An example of non-Darwinian evolution is the emergence of the deuterostomes from the protostomes by a flip of the antero-posterior body axis by 180 degrees and a flip of the dorso-ventral axis by 180 degrees. A second example is the origin of the Bilaterian animals by a sudden duplication of the animal by mirroring across the right left axis as opposed to a gradual adaptive evolution of a duplicated side over millions or even thousands of years. The new group of animals emerges abruptly in an instant of embryogenesis with a massively pleiotropic (multiple effects) change in the morphogenetic genes. Variation and natural selection play no role in this innovation. Darwinian evolution then acts to fine tune and optimize. Non-Darwinian evolutionary events may be relatively very rare, but play a major role in establishing new types of animals.

Nonhuman Primates – A term for all primates excluding whichever species we consider to be human. Typically this means prosimians, monkeys and apes.

Notch – A gene product that is involved in the process of separation of body segments from each other during the process of segment formation in the embryo.

notochord – A long tube oriented along the cranio-caudal axis of an organism that is typical of the Phylum Chordata. A remnant of the notochord occurs in the intervertebral disks in most vertebrates (see figure 7-4).

nucleated – Cells that have nuclei that localize and contain the cell’s genes. A key feature of the Eukaryotes.

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ontogeny – An old term for embryologic development.

Opisthokonta – A group of multi-cellular organisms that includes animals and fungi, but excludes plants.

oral-aboral – A description of the longitudinal axis of an animal as opposed to cranial-caudal that makes reference to the mouth being at the head and uses “Aboral” instead of referring to the anus at the opposite end of the body axis.

organelles – Functioning internal components of a cell.

organism – Any living biological entity.

Ornithischia – One of the two major groups of dinosaurs.

orthograde – A term used to describe upright posture in the hominoid primates.

Osiris – Egyptian god of the underworld. According to Egyptian mythology, he was resurrected by reassembly of his spine by his wife/sister Isis and the inventor god of medicine and science Thoth. He had been killed, then dismembered by his jealous brother Seth.

ossification – The process of bone formation.

Paleocene – The first geologic era of the Cenozoic, extending from 66 to 58 million years ago.

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palmigrade – Walking on the palms of the hand (see figure 10-1A).

Pan troglodytes – The chimpanzee.

Papyrus of Ani – A well preserved copy of the “Book of The Dead” or “The Book of Going Forth by Day”

parabronchial – A description of structure and function of the lungs of birds that allows for continuous forward flow of gases as opposed to the alternating intermittent (in and out) system used in mammalian (broncho-alveolar) lungs (see figure 8-3E).

paraphyletic – A group of animals that is improperly named from the point of view of cladistics because it excludes a sub-group. Dinosaurs are paraphyletic because the term excludes the birds.

pararthrum – The articulation point on the lateral aspect of the vertebra that articulates with the more ventral rib head, the capitulum (see figure 8-6).

pedicle – A pair of structures on the right and left sides of a vertebra that connect the laminar arch to the vertebral body (see figure 9-2A).

perissodactyls – A group of ungulate animals with a odd-numbered or single digit foot. This group includes the horse and the rhinoceros.

peristaltic – A pattern of movement of an animal or an organ within an animal (such as the digestive tract) that involves a wave progressing muscle activation along the length of the animal or organ.

peritoneal – The space in the abdomen containing the digestive system.

phalanges – The knuckles of the fingers and toes.

Phanerozoic – The epoch of time that commences with the Cambrian 540 million years ago and extends to modern times (see Timeline). The preceding period of time is termed the Proterozoic.

phenetic – In systematic biology, a method of assessing the similarity between organisms through a mathematical analysis of their total measurable features.

phenotypes – The proteins, features, morphologies, and behaviors that result from the expression of genes.

photosynthesis – The process of formation of glucose from carbon dioxide and water that is carried out in plants and is energetically driven by the capture of energy from light in the chloroplasts.

Phyla – A higher level grouping of organisms that typically have a unique body plan. There is no necessary objective basis for determining which animals are so different as to warrant assignment as a phylum, but there is nonetheless general agreement on most of the existing phyla.

phyletic gradualism – Gradual change in the morphology of a species across time without the separation of a new species.

PhyloCode – A proposed system of naming organisms employing a sort of bar code or numerical system that would replace the current Linnaen system.

phylogeny – A map of the relations among the various levels of biological groups and species in a clade.

placental mammals – The eutherian mammals whose young develop in the uterus, nourished by the placenta.

plantigrade – Walking on the soles of the feet

pleiomorphic – Having multiple different morphologies. Also used to describe multiple morphologic effects from some types of genetic mutations.

pleiotropic – A genetic change having multiple different effects.

plesiomorphic – A character or feature that displays the ancestral or more primitive version by comparison with the derived or modified version of the character state.

pleurapophysial – A type of lumbar transverse process that is a serial homolog of the ribs.

pleurocentrum – The vertebral body of nearly all existing amniotes is made up entirely from the pleurocentrum, but some early tetrapods had vertebral bodies dominated by the intercentrum. Small intercentra occur in some living mammals (see figure 8-5A).

Pliocene – A geologic time period (epoch) extending from 5 to 2 million years ago (see Timeline).

Plio-Pleistocene hominids – This includes Australopithecus as well as all of the species of Homo. These species occur between 5 million years ago and the beginning of the Holocene 11,500 years ago with the most recent major glacial retreat.

Plutarch – A roman historian.

point mutation – A single change in the DNA of a species affecting a single nucleotide pair.

polyphyly – A group name that involves member with different ancestors. This is universally considered an error in classification. An early example corrected by Linnaeus was the inclusion of whales and dolphins with fishes rather than with mammals.

Polypterus – A species of fish discovered by Etienne Geoffroy Saint-Hilaire in the late 1790’s that was capable of breathing air with its simple lungs and capable of walking across land with four of its fins. It’s discovery played a major role in the emergence of the concept of evolution (see figure 3-1).

population genetics – The mathematical and biological discipline of evaluating the numerical progress of the relative frequency of various genes and alleles in a population of interbreeding organisms.

postcranial – Referring to the anatomy of an organism other than the head.

presomitic mesoderm – The embryonic tissue composed of mesoderm – the source of muscle and bone – that is in the region of the embryo that will subsequently be divided into somites by the segmentation process.

primates – A group of mammals that includes prosimians (lemurs and galagos), tarsiers, monkeys, apes, and humans (see figure 10-4).

proconsulid – A group of hominoids from the Miocene that share several features with existing hominoids – such as the Y-5 molar cusp pattern – but which do not share the major vertebral transformation underlying upright posture that is seen in hominiformids such as the existing apes and humans. This includes species of Proconsul and  Nachalopithecus.

prokaryotic – A group of organisms whose DNA is not enclosed in  a nucleus – includes the Bacteria and the Archaea. The viruses are not included as they are not considered capable of independent life and reproduction.

pronograde – A posture during quadrupedal locomotion in which the body is oriented parallel to the ground (see figure 10-1A).

prosimian – A (paraphyletic) group of primates that includes lemurs, lorises and galagos that can also be described as the strepsirrhines as well as the tarsiers. The tarsiers are actually in the haplorrhine group along with monkeys, apes and humans but are referred to classically as prosimians. The simiiforme group includes the platyrrhines (new world monkeys) and the catarrhines (old world monkeys, apes and humans) but does not include any prosimians (see figure 10-4).

protein – A macromolecule polymer composed of multiple amino acids. They may be structural, enzymatic, or regulatory and the sequence structure of each kind of protein is specified by a gene or genes.

Proteus – A figure from Greek mythology capable of assuming any form. Goethe used this term to describe his concept of being able to compose any type of organism by assembling the relevant monomers – the leaf for plants, the segment for insects, the vertebra for vertebrates.

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quadrumanual – A description of the locomotion style of Orangutans who seem to make equal hand-and-arm-like use of all their extremities as they travel through trees.

quadrupedal – Walking on all fours (see figure 10-1A).

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radially symmetric – In biology a description of the Cnidaria and Ctenophores such as jellyfish that is an alternative to the bilateral symmetry seen in the Bilateria such as insects and vertebrates.

Radiata – A group name for non-bilaterian animals that display radial symmetry.

rare elements-earth –  A group of elements that includes the lanthanoid series as well as the (IUPAC) Group IIIb elements scandium and yttrium. They have many chemical similarities and tend to produce trivalent cations. They are actually not very rare in the earths crust when compared to elements such as silver or gold.

ray-finned fishes – The Actinopterygii group includes most fishes in the bony fish group (Osteichthyes) and exclude only the very few species of fleshy finned fishes or Sarcopterygii (which are more closely related to land tetrapods). The other type of living fish not included are the sharks (Chondrichthyes – cartilaginous fishes).

reptile – A (paraphyletic) group that refers to the sauropsid groups of turtles, lizards, snakes and archosaurs as well as to the synapsid reptiles such as the extinct pelycosaurs and therapsids. The term excludes the birds and the mammals. An alternate term that includes all the reptiles as well as birds and mammals is the amniotes.

retroviral RNA – The genome of retrovirus is stored as RNA rather than as DNA as in most other life forms. The RNA is copied into DNA by reverse transcriptase and then inserted into the host cells DNA where it can be copies and transcribed into RNA by the host’s proteins to produce the genomes and structural parts for new viruses.

reverse transcriptase – An enzyme used by retroviruses to copy their RNA genome into DNA. Other animals have reverse transcriptase enzymes such as telomerase which helps maintain the telomere “caps” on the ends of chromosomes.

RNA – A nucleic acid polymer that is used to carry information transcribed from the DNA of the genes in the nucleus, out into the cells cytoplasm, where it is anchored to ribosomes and translated into protein sequences. RNA also holds the genomic information in retroviruses and is used as a structural element in some cellular organelles involved in nucleic acid packaging and regulation.

Rosetta Stone – The first trilingual monument discovered that displayed a text in Egyptian hieroglyphics, demotic Coptic-style Egyptian language, and Greek. It led to the decipherment of Egyptian hieroglyphics after its discovery during Napoleon’s invasion of Egypt in 1799.

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sacrum – A group of vertebrae – usually fused together – that articulate with the hip bones.

sarcopterygians – Fleshy finned fishes. There a very few surviving species, but this group is ancestral to the land vertebrates.

Saurischia – A (paraphyletic) group of dinosaurs that includes the Theropods (Tyrannosaurus as well as the ancestors of birds).

scandium – A Group IIIb element that is included along with the lanthanoid elements and yttrium as a rare earth element.

scapula – The shoulder blade.

sedimentary – Rocks that were formed by the deposition of materials on the shore of an ocean.

segment – In developmental biology, an individual monomer or module that has an identity along the cranio-caudal axis specified by Hox genes.

segmentation – The process of separating the segments from each other during embryogenesis.

SEM – Scanning electron microscope – photographs produced with this system often have a dramatic three dimensional quality.

serial homology – The relationship of anatomical structures appearing with closely similar appearance and location in successive segments of a multi-segmented organism.

somites – Modules or monomers that are segmented along the cranio-caudal axis in vertebrates. Each gives rise to a myotome that forms that segment’s muscles and a sclerotome that forms that segment’s skeletal structures (see figure 7-4).

somitomeres – A still controversial description of what appear to be somite-like structures in the head region of vertebrate embryos.

speciation – The process of separation of two populations of one species into two separate daughter species.

species – A distinct group of individual organisms that maintains a biological coherence but which can be defined in several different ways. In a biological species concept (Ernst Mayr), we can distinguish living species by the barrier to interbreeding that separates their gene pools. There are also cladistic,  chronological and morphological definitions that are applied both in paleontology and in regard to existing species.

sperm – The motile carrier of the fathers contribution to the genetic make up of prospective new individual, capable of fertilizing a same species egg to produce a non-sterile, reproductively capable offspring.

spider segmentation – The process of segmentation in spiders. Of special interest because it employs genes that are quite similar to those used in vertebrate segmentation.

spinal cord – The portion of the central nervous system extending longitudinally along the body between the brain and the peripheral nerves.

spinous process – A midline bony projection on the dorsal aspect of the vertebral lamina.

styloid process – In anatomy, one type of styloid process is seen in therian mammals where it originates from splitting of the laminapophysis and is directed caudally in a position just lateral to the caudal facet joint or post-zygapophysis (see figure 9-2).

stylo-zygoid contact – An impact between the styloid process of a therian mammal and the prezygapophysis (cranial facet) of the following vertebra (see figure 9-6).

survival of the fittest – A principle aspect of Darwin’s theory of evolution. Since reproduction can produce a vast number of individuals that exceeds the environments ability to support them, some will die and some will survive to reproduce. Darwin suggested that those individuals whose inherited features gave them some advantage in the competition for scarce resources would be most likely to survive. This would result in a pruning of the range of variation in the genes of the species producing directed evolution across time that is called adaptation. This is the methodology of natural selection.

symplesiomorphy – A shared ancestral character state as defined in cladistic nomenclature.

synapomorphy – A shared derived or new character state as defined in cladistic nomenclature (see figure 5-3).

synapsid – A group of reptiles including the pelycosaurs and therapsids out of which the mammals emerged.

systematics – The science of studying and describing the range of individuals morphologies that constitute a species and of determining the relationships among species (also taxonomy).

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taxon – A group of organisms defined as a species, clade or other level of biological grouping.

teleology – The idea that every aspect of every animal must have a function – usually because of the argument that god would not have done otherwise. It is similar to the concept of adaptation which supposes that natural selection will require all features of an animal to serve some beneficial function.

terminal addition – A common characteristic of bilaterian animals in their embryology. They extend linearly from a cranial towards a caudal direction. In many cases, segmentation of the caudal extension then takes place.

tetrapod – A group of vertebrate animals that are distinguished from their fleshy finned fish ancestors (sarcopterygians) and which includes the amphibians, reptiles, mammals and birds.

therians – A group of mammals originating in the Cretaceous era that includes both the eutherian (placental) and the metatherians (marsupial) mammals.

thoracic – Vertebral segments in therian mammals that bear ribs and are distinguishable from lumbar vertebrae which typically have lumbar transverse processes but no ribs.

thorax – A region of the body in therian mammals that is separated from the abdomen by the muscular diaphragm and which is engaged in the mechanics of ventilation as well as being the site of the heart. This term can be used to describe similar regions in various other vertebrate and invertebrate groups.

Thrinaxodon – A cynodont genus  from 230 million years ago that is classed as a synapsid mammal-like reptile. It is well documented by complete fossils and it is a near relative of groups at the origin point of the mammalian clade.

transmutation – Changing from one thing into another. The term was used to describe the efforts of medieval alchemist to convert “base metals” into gold, but also describes what takes place in nuclear reactions when one element changes into another through fission or fusion of the atomic nucleus. This also describes the key claim of Darwinian evolutionary theory – that one species can change into a different one over time due to the effects of natural selection.

tRNA – A type of RNA (t = transfer) that attaches at one end to a specific amino acid monomer and aligns to a specific sequence on an mRNA (m=messenger) transcribed from a gene. It thereby accomplishes translation of the nucleic acid code sequence to the protein sequence.

Troglodytian Model – A widely accepted theory of human evolution that advocates a stage of quadrupedal knuckle-walking (chimpanzee-like) interposed just in advance of the origin of upright bipedalism in humans after the chimp human split six million years ago. This book, (the Upright Ape) proposes an alternative Humanian model in which suggests that human-like upright bipeds have existed from 22 million years ago and that knuckle-walkers are descended from human-like ancestors.

typology – A category of thought or philosophy in which groups or classes of individuals are considered as represented by a typical or “type” specimen. Michael Ghiselin has been a prominent advocate of considering species to be represented as the total range of examples presented by all the individuals in the species rather than by a type specimen.

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Undulated mutation – An alteration in the Pax1 gene of mice that results in several changes in body form that are reminiscent of the differences between hominiformid an proconsulid hominoids.

undulation – A pattern of movement or locomotion in which a wave of alternating muscle contraction from left to right is used to produce movement. This is used by many vertebrates such as fish, lizards, and snakes, but is suppressed in mammals, birds and possibly in dinosaurs as well (see figure 8-3F).

ungulate – A general term for mammals that walk on their tips of their fingers and toes. It is not a usable term from a cladistic point of view, but it refers to artiodactyls (cloven hoofed animals such as sheep, camels, and antelopes), perissodactyls (horses and rhinoceroses), and the Paenungulata (elephants).  The Paenungulata, in particular, are not closely related to the other ungulate groups among the mammals.

Urbilaterian – The theoretical original ancestor of the Bilaterian group that includes insects and vertebrates. This individual presumably suffered a dramatic pleiotropic mutation that duplicated the organism across the right left axis.

urkaryote – The theoretical original ancestor of all nucleated cells. This may have been a prokaryote that developed an endosymbiont relationship with another kind of prokaryote that became the nuclear organelle.

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variation – In biology, this typically refers to the various phenotypes produced by the various alleles and versions of a gene in the gene pool of a species.

ventilation – In biology this term is often applied to the mechanics of moving air in and out of the gas-exchange surfaces of the lungs.

ventral – A direction in biological descriptions of Bilaterian organisms that can describe the side of the animal that faces the ground during usual locomotion.

vertebra – A bone found in most vertebrate animals that is composed of a centrum (body) that is the major force transmitting component, an arch of bone or bones that reaches over and across the neural elements that are dorsal to the vertebral body,  and various processes or extensions depending on the kind of vertebrate. These repeat down the length of the animals and often demonstrate regional specializations along the cranio-caudal axis. These specializations are moderated by the same Hox genes that control regional specialization and differentiation of insect segments (see figure 9-2).

vertebrate – A group of animals (sub-phylum) within the deuterostome phylum Chordata that have vertebrae. This includes the fish, amphibia, reptiles, mammals and birds.

virus – A small biological entity that relies on a host organism to replicate, transcribe and translate its genome. It is capable of causing “horizontal gene transfer” – the transmission of a gene from one kind of organism to another where the two may be widely unrelated.  They may cause various level of disease or be fatal as they engage the services of their host.

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Y-5 – A description of a pattern of molar cusps that distinguishes hominoids from the ancestors of cercopithecoids (old world monkeys) among the catarrhine primates.

ytterbium – A Group IIIb element (IUPAC) that is included along with scandium and the lanthanoids in the “rare earth elements”. Like the other elements in this group, it tends to form trivalent cations.

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zoology – The study of animals.