This material is from the 4th edition of The Zebrafish Book. The 5th edition is available in print and within the ZFIN Protocol Wiki.


Modified from: Kimmel et al., 1995. Developmental Dynamics 203:253-310. Copyright © 1995 Wiley-Liss, Inc. Reprinted only by permission of Wiley-Liss, a subsidiary of John Wiley & Sons, Inc.

actinotrichia: unsegmented collagenous fin rays of the embryo and early larva, replaced later by the lepidotrichia, the definitive segmented bony fin rays

adaxial: paraxial mesoderm subregion developing just adjacent to the chorda mesoderm

animal pole: location on the egg where the polar bodies emerge, corresponding to the point of fertilization in fish like zebrafish, just below where the sperm penetrates the chorion through the micropile (passage way)

animal-vegetal axis: a line passing through the animal and vegetal poles of the embryo before the end of epiboly

anterior: towards the front (or head)

anterior posterior cardinal vein: see cardinal vein

anterior horn: the distinctive anterior region of the ventral stripe of melanophores, developing between the ear and eye

anterior-posterior (AP) axis: the principal axis of the embryo, here synonymous with rostrocaudal axis and embryonic axis

aorta: see dorsal aorta

aortic arch: artery leading from the ventral aorta to the paired radix (root) of the dorsal aorta, or, for the first two arches, to the internal carotid artery; an aortic arch develops in all but the most posterior of the seven pharyngeal arches, and the last four will carry the blood supply to and from the gills

AP: anterior-posterior

atrium: heart chamber collecting venous blood from the sinus venosus and delivering it to the ventricle; generates the first of each (doubled) heart beat

axial hypoblast: hypoblast that consists of mesodermal and probably endodermal precursor cells developing in the dorsal midline; includes prechordal plate and chorda mesoderm

axial vein: unpaired vein in the caudal trunk leading from the caudal vein and to the left and right posterior cardinal veins

axis: a line, or alternatively shorthand for the anterior-posterior or embryonic axis

bauplan: hypothetical basic or ancestral blueprint for developmental patterning, most often used with reference to the whole embryo pattern at the phylotypic stage

blastoderm: cellular part of the embryo, excluding the yolk cell, derived from the blastodisc by early morphogenesis; refers particularly to the time when the cell array is sheet-like, between 30%-epiboly and the end of gastrulation

blastodisc: (-disk) dome of cytoplasm (disk-like in the case of larger teleost eggs such as Fundulus and Salmo) that segregates from the yolk towards the animal pole during and after the one cell-stage, and which undergoes cleavage

blastomere: a cell arising during cleavage; the term encompasses the partially cleaved, incomplete "cells" at the blastodisc margin before they collectively form the yolk syncytial layer in the midblastula

blastula: classically the single-layered hollow ball of cells formed by cleavage in organisms that show this developmental style; here used to mean a stereoblastula, not hollowed-out, and as a descriptor for the period of development when the blastodisc begins to look ball-like, at the 128-cell stage through the time of onset of gastrulation

blood island: nest of developing blood cells arising late in the segmentation period from the intermediate mass, and located in the anterior-ventral tail, just posterior to the yolk extension

Brachet's cleft: the visible division between epiblast and hypoblast in the gastrula

branchial arch: gill arch; the last five of the set of seven pharyngeal arches; the numbering system can be confusing; generally branchial arch #1 is the first gill arch, or the third pharyngeal arch, but some authors do not follow this convention

cardinal vein: bilaterally paired longitudinial vein; the anterior cardinal returns blood from the head, and the posterior cardinal returns it from the trunk; these two vessels join together on each side as the common cardinal vein (duct of Cuvier; misnamed the vitelline vein) that leads across the yolk cell to the heart's sinus venosus

carotid artery: see internal carotid artery

caudal: pertaining to the tail, or the posterior direction

caudal artery: extension of the dorsal aorta in the tail

caudal vein: vein in the tail returning blood from the trunk and tail to the heart, leads directly into the axial vein in the posterior trunk

central canal: fluid-filled narrow cavity in the spinal cord

central nervous system: the brain and spinal cord

ceratobranchial cartilage: cartilaginous element present in a branchial arch at the end of embryogenesis; other cartilages will form in these arches later in the young larva

ceratohyal cartilage: massive ventral cartilage of the hyoid arch, generally supposed to be serially homologous to the ceratobranchial cartilages, and perhaps to Meckel's cartilage

cerebellum: specialized brain region derived from the dorsal metencephalon (anterior hindbrain, and perhaps including posterior midbrain) and becoming distinctive late in the segmentation period

chondrocranium: the initially cartilaginous region of the skull that eventually surrounds the brain and forms capsules over the sensory organs, including the olfactory organ, eye and ear; distinct from the dermatocranium (skull bones forming without cartilage models, and mostly after embryogenesis) and the splanchnocranium (the portion of the head skeleton developing from the pharyngeal arches)

chorda mesoderm: the notochord rudiment

chorion: the egg shell

cleavage: an early mitotic cell division occurring in the blastodisc, special in that the cell cycles are short in length, are not accompanied by cell growth during interphase, and occur synchronously or metasynchronously with other cleavages of the same number; in the staging series, the cleavage period refers to the period of development encompassing the first 6 six zygotic cell cycles

cleithrum: transversely oriented bone connecting the occipital region of the skull dorsally and pectoral girdle ventrally; appears near the end of embryogenesis

coelom (coelomic cavity): fluid-filled mesodermally lined cavity separating visceral organs including the heart from the body wall

common cardinal vein: see cardinal vein

conus (bulbus) arteriosus: muscular heart region leading blood out of the heart to the ventral aorta

convergence: deep cell movement toward the dorsal side of the embryo during the gastrula and early segmentation periods

deep cell, a cell in the blastodisc (first at the 64-cell stage) or blastoderm that is completely covered over by other cells, the outermost being cells of the enveloping layer

deep cell layer (DEL): a multilayer of deep cells of fairly uniform thickness that forms during early epiboly (at dome stage; upon conversion of the blastodisc to the blastoderm); during gastrulation the DEL gives rise to the epiblast and hypoblast

DEL: deep cell layer

diencephalon: the more posterior and ventral of two forebrain neuromeres, the other being the telencephalon; major derivatives are the eye cups, the brain pretectal region, the thalamus, hypothalamus, and epithalamus (including the habenula and epiphysis)

dorsal: toward the back (the side opposite to the belly)

dorsal aorta: principal unpaired, median artery of the trunk, leading from the paired roots (radices) of the dorsal aorta to the caudal artery

dorsal stripe: longitudinal arrangement of melanophores along the dorsal side of the embryo, underlying the median fin fold; the cells lie in the midline in the anterior trunk and tail, and are present bilaterally in the head and posterior trunk

dorsal-ventral (dorsoventral): axis passing from the back to the belly; within a sagittal plane and at right angles to the anterior-posterior axis

duct of Cuvier: see cardinal vein

EL: embryo length

embryo length (EL): at any stage the embryo's longest linear dimension

embryonic axis: see anterior-posterior axis

endothelium: epithelial lining of any blood vessel including the heart

enveloping layer (EVL): outermost monolayer of cells surrounding the embryo that become very flattened in the blastula and give rise to the periderm

epaxial muscle: somite-derived body wall muscle present dorsal to the horizontal myoseptum

epiblast: the outer of the two layers of the blastoderm that form during gastrulation, corresponding to primitive ectoderm during gastrulation and to the definitive ectoderm after gastrulation

epiboly: the thinning and spreading of both the YSL and the blastoderm over and across the yolk cell, eventually encompassing the yolk cell completely; epiboly begins at dome stage, converts the blastodisc to the blastoderm, and is considered to be over when the yolk plug closes over (at 100%-epiboly)

epiphysis: a circumscribed swelling, includes the pineal primordium that appears late in the segmentation period in the dorsal midline of the diencephalon

epithelium: a compact and sheet-like arrangement of cells, polarized with the apical surface to one side (primitively the outside) and the basal surface to the other

evacuation zone: the anterior-ventral region of the mid and late gastrula that becomes cell-poor, as cells leave by both epiboly and convergence

EVL: enveloping layer

extension: lengthening of the embryonic axis, principally by deep cell repacking (by intercalations) and occurring during the gastrula and early segmentation periods

external yolk syncytial layer (E-YSL): portion of the YSL that is outside of the blastoderm margin during epiboly

extraembryonic: making no direct cellular contribution to the body of the embryo

E-YSL: external yolk syncytial layer

face view: side view along the odd-numbered cleavage planes during the cleavage or blastula periods

fate map: map at a early developmental stage (here at gastrula onset) of what cells normally will become

fin fold: the rudiment of the median unpaired fins, appearing in the late segmentation period, prominent throughout the rest of embryogenesis

forebrain: the most anterior region the brain including both the telencephalon and diencephalon; we have not observed an early transient stage when the forebrain is distinguished from the midbrain but has not subdivided, that would correspond to the prosencephalon in tetrapods

gastrula: classically a postblastula stage in which an archenteron (primitive gut or gastrocoele) forms by invagination or involution of cells through a blastopore and when the germ layers and embryonic axis appear; the zebrafish forms neither an archenteron nor a blastopore, and here the term refers to the roughly equivalent period of development, beginning at the onset of involution (at the 50%-epiboly stage) that produces the two primary germ layers, the epiblast and hypoblast, and during which the definitive embryonic axis forms by convergence and extension movements

gastrulation: morphogenesis during the gastrula period

gill arch: one of the subset of pharyngeal arches (pharyngeal arches 3-6, or branchial arches 1-4) that will develop gills

gill filament: branched region of the gill where respiratory exchange takes place

hair cell: specialized neuronal receptor cell of the lateral line and acoustico-vestibular systems

hatching gland: a transversely oriented set of cells located deep to the EVL on the pericardial membrane, especially prominent during pharyngula period because of the brightly refractile cytoplasmic granules (containing hatching enzymes) of the principal cells of the gland

head-trunk angle (HTA): in side view, the smaller angle between the head axis (a line through the middle of the ear and eye) and the trunk axis (a line parallel to the long axis of the notochord at about somites 5-10

hindbrain: the most posterior of the three principle regions of the brain, forming the rhombencephalon and all or most of the metencephalon

horizontal: during cleavage and blastula periods a plane perpendicular to the animal-vegetal axis; later a longitudinal plane parallel to the embryonic axis and perpendicular to the dorsal ventral axis, i.e. at right angles to both transverse and sagittal planes

horizontal myoseptum: a connective tissue partition developing at the apex of the chevron-shaped myotome and separating dorsal (epaxial) and ventral (hypaxial) body wall muscle masses

HTA: head-trunk angle

hypaxial muscle: somite-derived body wall muscle present ventral to the horizontal myoseptum

hyosymplectic (hyomandibular, epihyal) cartilage: the dorsal cartilage forming in the hyoid arch

hyoid arch: the second pharyngeal arch, forming the operculum and secondary supportive elements of the jaw

hypoblast (mesendoderm): the inner of the two layers of the blastoderm that forms during gastrulation and give rise to the definitive mesoderm and endoderm

hypothalamus: a specialized brain region of the ventral diencephalon arising near the end of the segmentation period; the embryonic hypothalamic region will give rise to the posterior pituitary gland as well as a number of brain nuclei

incomplete cleavage: see meroblastic cleavage

intermediate mass: the very early blood rudiment located deep to the somites in the posterior trunk at a stage before the blood cells collect into the (more prominent) blood island

internal carotid artery: artery originating at the junction of the first two aortic arches and supplying the anterior brain

internal yolk syncytial layer (I-YSL): the portion of the YSL that lies deep to the blastoderm during epiboly

involution: deep cell movement at the blastoderm margin in which the DEL folds inwards and back upon itself, producing the germ ring and its two primary germ layers, the epiblast and hypoblast

iridophore: reflective pigment cell

I-YSL: internal yolk syncytial layer

keel: see neural keel

Kupffer's vesicle: small but distinctive epithelial sac containing fluid, located midventrally posterior to the yolk cell or its extension, and transiently present during most of the segmentation period

lateral: away from the midline

lateral patch: a prominent collection of iridophores on the dorsolateral yolk sac flanking the position of the developing swim bladder

lateral stripe: melanophore stripe along the horizontal myosepta

lens placode: ectodermal primordium of the lens of the eye

mandibular arch: first (most anterior) pharyngeal arch, forming the principal elements of the jaw of the early larva

mandibular cartilage: see Meckel's cartilage

marginal blastomere: cell (incompletely cleaved before the YSL forms), located in the surface layer (EVL) just at the rim of the blastodisc

MBT: midblastula transition

Meckel's (mandibular) cartilage: ventral cartilage of the mandibular arch forming the principal support of the (lower) jaw

medial: toward the midline

median: at the midline

mediolateral: horizontal axis oriented perpendicular to both the anterior-posterior and dorsal-ventral axes

mediolateral intercalation: ordered cellular repacking along the mediolateral axis brought about by interdigitations of deep cells during the gastrula and early segmentation periods; produces convergence and extension

melanophore (melanocyte): a neural crest-derived cell containing black melanin pigment

meroblastic (incomplete) cleavage: cell division in which sister cells are only partially separated from one another by cytokinesis; includes all of the early cleavages, and also occurs along the blastodisc margin in the late cleavage and early blastula periods

mesencephalon: see midbrain

mesenchyme: a mesh-like cell arrangement, less compact than an epithelium

mesendoderm: see hypoblast

metasynchronous: occurring in a nearly synchronous wave

metencephalon: brain region in the neighborhood of the first rhombomere; gives rise to structures including the fourth cranial (troclear) motor nucleus, the cerebellum dorsally, and the interpeduncular nucleus ventrally

midblastula transition (MBT): the time of increase in cell cycle length above the rapid rate characterizing the cleavage period, beginning at the 10th zygotic cycle; at the MBT cells also begin to divide less synchronously, and motility and zygotic transcription are first observed

midbrain (mesencephalon): the brain region between the forebrain anteriorly and the hindbrain posteriorly, including the tectum dorsally and the midbrain tegmentum ventrally

midsagittal plane: the plane of bilateral symmetry, located at the midline

myomere: see myotome

myotome: portion of the somite giving rise to body wall muscle masses

neural crest: a cell population arising from the dorsolateral aspect of the central nervous system primordium during the segmentation period, and later migrating along stereotyped pathways to give rise to a diverse and well-defined set of cell types including pigment cells, peripheral neurons and glia, and head cartilage

neural groove: a midsagittal depression on the surface of the anterior neural plate present during the early segmentation period

neural plate: the earliest recognizeable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium

neural keel: an intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section

neural retina: the sensory retinal epithelium, developing from the inner layer of the optic cup; the neural retina forms prominent sublayers during the hatching period, including the inner ganglion cell layer, interneuronal layers, and the outer layer of photoreceptor cells just deep to the retinal pigment layer

neural rod: an intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube

neural tube: cavity-containing primordium of the central nervous system, developing from the neural rod in the late segmentation period

neuromast: volcano-shaped lateral line sensory organ located in characteristic positions within the skin epithelium and containing hair cells and their support elements

neuromere: a brain subdivision recognized morphologically as a swelling bounded by constrictions

notochord: rod-like principal supportive element of the embryo and larva, present in the midline just ventral to the neural tube, and differentiating during the segmentation period to form large vacuolated principal cells and a surrounding thin epithelial notochord sheath

optic cup: two-layered stage of eye development arising from the seemingly unlayered optic primordium; the inner layer develops as the neural retina, and the outer layer forms the pigmented retina

optic primordium: lateral outgrowth from the forebrain that will form the eyeball (excluding the lens); equivalent to the optic vesicle of tetrapods, but apparently not a hollow structure; develops into the two layered optic cup

optic tectum: the roof of the midbrain, morphologically visible by the end of the segmentation period

otic capsule: region of the chondrocranium surrounding otic vesicle

otic placode: primordium of the ear epithelium before it hollows into the otic vesicle, present beside the hindbrain rudiment in the midsegmentation period

otic vesicle: epithelial sac present beside the fifth rhombomere; forms the semicircular canals dorsally and the otolith organs ventrally, and houses the acoustico-vestibular sensory epithelia (maculae) of hair cells

otic vesicle length (OVL): a staging device or index defined as the number of additional otic vesicles that could be fit in between the otic vesicle and the eye

otolith: brightly refractile stone-like organ within the otic vesicle and positioned over a sensory macula; two form in each vesicle during the late segmentation period

OVL: otic vesicle length

palatoquadrate: see quadrate

paraxial hypoblast: hypoblast that is mainly or entirely mesodermal, positioned laterally to the axial hypoblast; forms somites and their derivatives in the trunk and muscles and endothelium in the head

periblast: archaic term for the YSL

pericardium: portion of the coelomic cavity present as a distinctive chamber surrounding the heart

periderm: flattened tightly sealed epithelial monolayer of specialized impermeable cells covering the entire embryo after epiboly ends, and representing the sole derivative of the EVL

peripheral nervous system: nervous structures including ganglia outside of the central nervous system

pharyngeal (visceral) arch: a segment of the lateral wall of the pharynx that will form jaw structures (anterior two arches ) or gill structures (posterior 5 arches); an arch includes a compact mesenchyme lined by inner endoderm and outer epidermis; each arch is separated from neighboring arches by an endodermal outpocketing (a pharyngeal pouch) meeting a slight ectodermal inpocketing (a pharyngeal cleft) where a gill slit develops during the hatching period (except between the first and second arches)

pharyngula: generally, a vertebrate embryo that has developed to the phylotypic stage; in the series used as a period name to describe the second of the three days of embryonic development

pharynx: swollen region of the anterior foregut, posterior to the mouth and anterior to the liver; its walls form the jaws and gills

phylotypic stage: the stage at which the embryo develops features defining it as a vertebrate or chordate, including the notochord, neural tube, pharyngeal arches, somites and postanal tail

pillow: see polster

placode: a thickened or plate-like region within an epithelium

prechordal plate: axial hypoblast located anterior to the chorda mesoderm; the polster is its most anterior region

prim: see primordium of the lateral line

primary motoneuron: one of a subset of spinal motoneurons innervating body wall muscle that develop early and achieve large size; present in 3 or 4 identifiable pairs per spinal segment

primordium of the lateral line: placodally-derived rudiment of the posterior lateral line that during the pharyngula period migrates posteriorly through the skin overlying the horizontal myosepta and deposits neuromast primordia along the way; its progress is used as a staging index during the pharyngula period to define "prim" stages

polster (pillow): the hatching gland rudiment at the time it underlies the forebrain during the early segmentation period

posterior: toward the rear (or tail - not meaning towards the dorsal side)

posterior cardinal vein: see cardinal vein

pronephric duct: duct of the embryonic kidney, present bilaterally ventral to the somites and leading to the anal region where it empties separately from, and just posterior to the anus

pronephros: embryonic kidney, present at the level of the third somite

prosencephalon: see forebrain

quadrate (palatoquadrate): the dorsal cartilage (later ossifying) of the first pharyngeal arch forming the main part of the upper jaw skeleton and lateral part of the larval palate

radial intercalation: ordered cellular repacking among deep cells of the deep and shallow regions of the blastodisc, effecting epiboly and producing a uniformly thin blastoderm; begins during the late blastula period, and perhaps continues during gastrulation

reticular cell: see tail reticular cell

retina: the portion of the eye developing from the optic primordium and including the neural retina and the retinal pigment layer

retinal pigment layer (tapetum): a monolayer of pigmented epithelium covering the neural retina; develops from the outer of the 2 layers of the optic cup

rhombencephalon: hindbrain, or the division of the hindbrain posterior to the metencephalon and anterior to the spinal cord

rhombomere: hindbrain segment or neuromere

Rohon-Beard neuron: a primary sensory neuron present in the dorsal spinal cord of the embryo and early larva

rostral: toward the head, for the zebrafish embryo synonymous with anterior

rostral-caudal (rostrocaudal) axis: here synonymous with anterior-posterior axis

sagittal: a plane parallel to the plane of bilateral symmetry

sclerotome: medial ventral region of the somite that will form vertebral cartilages

segmental artery: artery leading from the dorsal aorta or caudal artery to the spinal cord; the arteries alternate in adjacent segments with segmental veins

segmental plate: unsegmented field of paraxial mesoderm present posterior to the somite file, from which somites will form

segmental vein: vein leading from the spinal cord to the caudal vein, axial vein, or posterior cardinal vein

segmentation: a repetition of elements, particularly along the AP axis; used in the series to define the period of development between the gastrula and pharyngula

sinus venosus: heart region collecting blood from the paired common cardinal veins and delivering to the atrium

somite: undifferentiated mesodermal component of an early trunk or tail segment or metamere, derived from paraxial mesoderm; forms the myotome, sclerotome and perhaps dermatome

stereoblastula: see blastula

subclavian artery: artery supplying the pectoral fin

subclavian vein: vein returning blood from the pectoral fin to the cardinal system

tail reticular cell: cell lining the vascular channel network in the posterior and ventral tail that connects between the caudal artery and vein, apparently specialized for phagocytic clearing of the blood

tectum: see optic tectum

telencephalon: the anterior and dorsal forebrain neuromere, includes the olfactory bulb

tier arrangement of blastomeres: horizontal rows of blastomeres as seen in a face view of the embryo during the cleavage and blastula periods; tiers are counted between the blastodisc margin and the animal pole as a staging aid

trigeminal ganglion: a prominent collection of touch-sensory neurons of the trigeminal or fifth cranial nerve, positioned beside the brain between the eye and the ear

trigeminal placode: the ectodermal rudiment of the trigeminal ganglion, distinguishable during much of the segmentation period

vegetal pole: location on the egg opposite to the animal pole, corresponding later to the point on the yolk cell furthest from the developing blastodisc

ventral: toward the belly (or yolk)

ventral aorta: outflow artery from the heart to the aortic arches

ventral stripe: melanophore stripe just ventral to the myotomes

ventricle: fluid-filled brain cavity; alternatively a heart chamber collecting venous blood from the atrium and delivering it to the conus arteriosus; the ventricle mediates the second and major component of each (doubled) heart beat

vertical: here meaning a plane parallel to the animal-vegetal axis during the cleavage and blastula periods

visceral: pertaining to the gut or endoderm or splanchnic mesoderm associated with endoderm

visceral arch: see pharyngeal arch

vitelline vein: see cardinal vein

xanthophore: a neural crest-derived cell pigmented yellow

yolk: nutrient store for embryonic development in the form of semicrystalline phospholipoprotein and contained within yolk granules

yolk ball: the anterior round region of the yolk cell present after the yolk extension forms during the segmentation period

yolk extension: the posterior elongated region of the yolk cell that forms during the segmentation period

yolk cell: giant syncytial uncleaved cell containing the yolk; underlies the blastodisc early, and becomes enveloped by the blastoderm during epiboly

yolk granule: membrane-bounded sac, of the order of 50 µm in diameter, containing yolk; yolk granules are packed densely in the interior of the yolk cell, deep to its syncytial layer, and make up the great bulk of its total volume

yolk plug: the bit of yolk cell protruding beyond the blastoderm margin in the late gastrula before epiboly is complete

yolk stripe: a late-forming melanophore stripe along the median ventral aspect of the yolk ball and particularly the yolk extension

yolk syncytial layer (YSL): peripheral layer of the yolk cell including nuclei and non-yolky cytoplasm

YSL: yolk syncytial layer

zygote: the fertilized egg, defining in the series the period between fertilization and the end of the first cleavage

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