List of transitional forms
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A transitional form is an organism that has features intermediate of its ancestors and progeny. The term is most common in evolution to refer to organisms that show certain features (wings, feathers, gills and so on) partly in development. In theory, every fossil is a transitional form if it has descendants and each living creature is a transition between its parent and its offspring. However, evolution is about the features of populations rather than individuals, and the transition at the species level can be too small to notice in fossils. So the list below concentrates on broad transitional features and the genus or larger group.
A fossil (and the organism it came from) is usually considered transitional with respect to just two groups. (If more than two are considered, then the definition of "transitional" is fuzzier.) Individual organisms (or individual species), considered by themselves, cannot be divided into "transitional" and "non-transitional", rather like how individual towns can be labeled "between" and "not between"; the term is relative. However, in cases where two groups are very populous or well-known, and all of the intermediate species have gone extinct, any intermediate organism's transitional nature becomes noteworthy and noticeable, and may hence be called "transitional" all by itself. To return to the analogy of geography, the United States has a region called "the Midwest" or (somewhat derogatory) "flyover country". Of course every town and region in the US is in the middle and to the West of somewhere, and can be flown over. But the reason the Midwest is singled out as a "transitional" region is that it lies between the more populous and city-strewn East and West Coasts yet itself is denser than the Great Plains to its own west.
While some of the fossilized species in this list may be direct descendants and direct ancestors of the forms on either side of the transition, most are in fact close relatives of the "true" ancestral species. This is because evolution produces a tree of life on which there are many paths "up", but forward in time there is only one true path "down", through the various parent species. (A mother species can have many daughters, but each daughter has only one mother.) The number of fossils directly ancestral to, for example, modern birds decreases as one travels down the geologic column. Alongside each of these true bird ancestors are dozens of fossilized cousin bird species whose lines eventually died out altogether, but whose morphology provides clues about the nature of the ancestral species.
Because of all this, the term transitional form is often used to mean organisms that lie between two groups as cousins, not just as ancestors. For example, the echidna is not ancestral to modern mammals, but retains features of the reptile-like mammals which other mammals (the therians) lost, and is therefore transitional between ancient reptiles and therian mammals. A generally interchangeable term is intermediate form. Most iconic transitionals are the close descendants or cousins of a directly ancestral species whose fossils have not been found, or which never fossilized to begin with. (Fossilization is extremely rare.)
According to creationists
According to creationists, each and every one of the following fossils is either misinterpreted by scientists, a fraud manufactured by scientists, or does not exist at all. They have been shown utterly wrong in this claim - so they keep claiming it anyway.
Creationists also define transitional forms in inherently absurd or vague ways that cannot be met by the evidence. For example, they may insist that each of a proposed transitional organism's parts (its legs, eyes, wings) should be "partially formed" instead of "fully formed", even if those parts have nothing to do with the transition. (For example, that an ape-human transitional form would have half-length limbs, or only one eye.) What "partially formed" means is not always clear.
Even more nebulously, it is argued that a true transitional would be an "incomplete creature", a fantasy that creationists will contrast with the known fossil record of "fully formed" or "fully functional" creatures. A similar idea is that "real" transitionals would be Frankenstein's monsters, stitched-together assemblages of the parts of the two species. (It is akin to asserting that evolution could not be real unless the Piltdown hoax was also real, or asserting that if teenagers were really between children and adults, they would have baby heads on adult bodies.) In short, if biologists believe the species's members were healthy enough to survive for more than a few days, then it can't be transitional, because it must have been "fully formed". The thinking here may be a product of biological essentialism — a thing is either A or B, and something "between" A and B is logically impossible or convoluted.
Some creationists propose that the common ancestor of two species would necessarily look like a blend of them, such as Kirk Cameron's infamous Crocoduck. This ignores that the evolutionary model involves traits arising without having to be present in the common ancestor. Otherwise, the world's earliest life forms would somehow look like combinations of every species alive today. Also, a given distant ancestor species with living progeny (for example, the reptilian ancestor of ducks and crocodiles) will also have many different-looking descendants, not just two. Evolutionary lines do not "run out" of divergences any more than the surname Smith would run out of acts of reproduction.
Another mistake/lie made by creationist is that a transitional fossil has to be the direct descendant of one species and the direct ancestor of another. What they do not understand is the true definition of a transitional form. A transitional form illustrates an evolutionary link, as it can have features of two species, but have no other species as descendants. For example, your mother would be a 'transitional form' between you and your grandmother, as she shares traits with both of you. However, if your mother had a sister, she would also be a "transitional form" between you and your grandmother, having traits from both of you.
For example, apes and humans split from a common ancestor seven million years ago and both lineages are still around.
For this reason the concept of "missing link" is a misleading one. A transitional form does not need to be a perfect halfway house directly linking one group of organisms to another. "It merely needs to record aspects of evolutionary change that occurred as one lineage split from another."
It is also sometimes argued that if key transitional traits of an intermediate species (for example, the wing claws of Archaeopteryx) have not completely disappeared today, the species is not transitional. (The ostrich has wing claws). Of course, biology is under no obligation to "clear the slate" and make it so that extinct species' traits are utterly foreign to us. To assume otherwise is to assume presentism, that there is something "special" about the modern day. Eventually, perhaps, ostrich claws will disappear -- will this make them "retroactively" transitional?
When all hope is lost, creationists call the intermediate a "mosaic species" that "doesn't prove anything", and point out that God can create whatever he wants.
The species listed here are all thought to be close relatives of species descending from the first forms in the list and ancestral to the last ones. Each list represents some branch on the tree of life, its members being the sub-branches and "twigs" extending from this branch.
Transitions in vertebrates before the Cenozoic
- This is a fairly incomplete list. Please help us expand it!
Invertebrate to Vertebrate
- Unnamed Upper (U.) Pre-Cambrian chordate — First to bear a primitive notochord; archaetypical chordate.
- Pikaia gracilens — Middle (M.) Cambrian chordate with lancelet-like morphology.
- Haikouella — Lower (L.) Cambrian chordate, first to bear a skull; archaetypical craniate.
- Haikouichthys — L. Cambrian quasi-vertebrate, intermediate in developing a vertebral column; archaetypical vertebrate. 
- Conodonts — U. Cambrian to Triassic quasi-vertebrates with spinal cord; "bug-eyed lampreys".
- Myllokunmingia — L. Cambrian vertebrate with primitive spinal column; oldest true crown-group vertebrate.
- Arandaspis — L. Ordovician vertebrate, armoured jawless fish (ostracoderm), oldest known vertebrate with hard parts known from (mostly) complete fossils.
Jawless Fish to Jawed Vertebrate
- Birkenia — Silurian primitive, jawless fish, a typical member of the Anaspida
- Cephalaspis — Silurian armoured jawless fish, archaetypical member of the "Osteostraca," sister group to all jawed vertebrates.
- Shuyu — Silurian to Devonian, armoured jawless fish belonging to Galeaspida, related to Osteostraca. Internal cranial anatomy very similar to the anatomy seen in basal jawed vertebrates. This similarity is directly implied with the translation of its name, "Dawn Fish," with the implication that it represents the "dawn of jawed vertebrates."
- Ptomacanthus — sharklike fish, originally described as an acanthodian fish: brain anatomy demonstrates that it is an intermediate between acanthodians and sharks.
- Cladoselache — primitive/basal shark.
- Tristychius — another sharklike fish.
- Ctenacanthus — primitive/basal shark.
- Paleospinax — sharklike jaw, primitive teeth.
- Spathobatis — Ray-like fish.
- Protospinax — Ancestral to both sharks and skates.
- Acanthodians — superficially similar to early bony fishes, and some have been identified as being the ancestors of sharks.
- Palaeoniscoids — primitive bony fishes.
- Canobius, Aeduella — palaeoniscoids with more advanced jaws.
- Parasemionotus — combination of modern cheeks with more primitive features, like lungs
- Oreochima — first teleost fish
- Leptolepids — vaguely herring-like ancestors of modern teleost fish. Lung modified into swim bladder.
- Amphistium and Heteronectes — percomorphs that demonstrate the transition of the eye location of flatfishes.
- Paleoniscoids — both ancestral to modern fish and land vertebrates
- Osteolepis — modified limb bones, amphibian like skull and teeth
- Kenichthys — shows the position of exhaling nostrils moving from front to fish to throat in tetrapods in its halfway point, in the teeth
- Eusthenopteron, Sterropterygion — fin bones similarly structured to amphibian feet, but no toes yet, and still fishlike bodily proportions
- Panderichthys, Elpistostege — tetrapod-like bodily proportions.
- Obruchevichthys — fragmented skeleton with intermediate characteristics, possible first tetrapod.
- Tiktaalik — a fish with developing legs. Also appearance of ribs and neck.
- Acanthostega gunnari—famous intermediate fossil. most primitive fossil that is known to be a tetrapod or four legged animal from the Upper Devonian of Greenland, which has shed significant light on the derivation and early evolution of tetrapods. It had legs and feet but was aquatic, not an amphibian.
- Ichthyostega — like Acanthostega, another fishlike amphibian
- Hynerpeton — A little more advanced than Acanthostega and Ichtyostega
- Labyrinthodonts — still many fishlike features, but tailfins have disappeared
- Gars — Fish with vascularized swim bladders that can function as lungs
- Lungfish and Birchirs — fish that have lungs
- Dendrerpeton acadianum
- Archegosaurus decheni
- Eryops megacephalus
- Amphibamus lyelli
- Doleserpeton annectens
- Triadobatrachus — a primitive frog.
- Vieraella — an early modern frog
- Karaurus — a primitive salamander
- Pappochelys rosinae — diapsid skull with expanded ribs and fused gastralia
- Odontochelys semitestacea — secondary loss of temporal fenestrae, partial formation of a turtle shell, showing how the hard underbelly, or plastron, formed first.
- Deltavjatia vjatkensis
- Protoclepsydrops haplous
- Adelobasileus cromptoni
- Morganucodon -- a transition between "proto mammals" and "true mammals".
- Steropodon galmani
- Vincelestes neuquenianus
- Pariadens kirklandi
- Kulindadromeus — A basal neornithischian (Ya know, Triceratops, Iguanadon, Hypsilophodon, and such) with feathers.
- Allosaurus — A large theropod with a wishbone.
- Aerosteon — A large theropod of the same lineage as the aforementioned Allosaurus that was discovered to have air sacs supplementing lungs, like modern birds.
- Compsognathus — A small coeleurosaur with a wishbone.
- Gigantoraptor — A large oviraptorosaur discovered brooding its nests in order to protect and incubate eggs.
- Mei — A troodont discovered sleeping with its head underneath its wing/
- Balaur — A large flightless bird that was wrongly thought to be a dromaeosaurid dinosaur..
- Sinosauropteryx — a basal coelurosaur discovered to be covered in feathers. It is also the first dinosaur to have its colour determined, thanks to preserved pigment structures in the feathers.
- Velociraptor — a famous dromaeosaurid discovered to have quill knobs on its wrists. For some odd-like reason, sadly. Everyone sees these things as mutant dragon-like things.
- Oviraptor — the first dinosaur discovered to
- Microraptor — a feathered bird with distinctly dinosaurian characteristics, such as its tail.
- Xiaotingia — slightly earlier than Archaeopteryx, slightly more like a dinosaur and less like a bird
- Archaeopteryx — the famous bird-with-teeth.
- Hesperornis — A diving seabird with prominent teeth. It's also completely flightless.
- Ichthyornis — A flying seabird with prominent teeth.
- Columba — One of many typical modern birds.
Transitional mammalian fossils
- Purgatorius — the earliest primate-like organism
- Plesiadapis — Mammal closely related to primates.
- Carpolestes — Mammal closely related to primates
- Archicebus — First euprimate, or something very similar to it.
- Omomys — Tarsier-like primate
- Eosimias — Basal anthropoid
- Amphipithecus — Another basal anthropoid
- Apidium — The first, primitive monkey.
- Propliopithecus — Primitive New World Monkey
- Darwinius masillae — a link between earlier primates and later ones.
- Dryopithecus Primitive ape.
- Proconsul Primate that is closely related to apes.
- Sivapithecus Primate closely related to the ancestors of Orangutans
- Djebelemur First lemuriform primate.
- Cantius Extremely primitive prosimian from the Early Eocene of North America.
- Teilhardina First North American primate.
Non-human primate to human
- Sahelanthropus — possible candidate for last human-chimpanzee common ancestor; from placement of skull possibly walked upright.
- Orrorin — possible human ancestor, may have walked upright as shown by shape of femur.
- Australopithecus — a genus of bipedal apes
- Australopithecus sediba — advanced Australopithecus showing more human features
- Kenyanthropus — a genus of bipedal apes that may have been the earliest known tool users; possibly the earliest member of the genus Homo
- Homo habilis — a transitional form from Australopithecus to later Homo
- Homo rudolfensis — a type of Homo habilis or a different species
- Homo ergaster — an early form of Homo erectus or a distinct species
- Homo erectus — a transitional form from earlier Homo to later Homo (Latin for "human") species
- Homo heidelbergensis — a possible common ancestor of modern man and Homo neanderthalensis  
- Homo neanderthalensis — Neanderthals interbred with modern humans multiple times.
- Homo floresiensis The infamous "hobbits" of Flores.
- Homo sapiens idaltu archaic subspecies of modern human, possibly ancestral to Homo sapiens sapiens (modern humans).
- Indohyus — a vaguely chevrotain-like or raccoon-like aquatic artiodactyl ungulate with an inner ear identical to that of whales.
- Ambulocetus— an early whale that looks like a mammalian version of a crocodile
- Pakicetus — an early, semi-aquatic whale, a superficially wolf-like animal believed to be a direct ancestor of modern whales.
- Rhodocetus — An early whale with comparatively large hindlegs: not only represents a transition between semi-aquatic whales, like Ambulocetus, and obligately aquatic whales, like Basilosaurus.
- Basilosaurus — A large, elongated whale with vestigial hind flippers: transition from early marine whales (like Rhodocetus) to modern whales
- Dorudon — A small whale with vestigial hind flippers, close relative of Basilosaurus.
Transitional plant fossils
- Cooksonia — early vascular plant
- Archaeopteris — early tree
- Williamsonia — an early flowering plant ("stem angiosperm")
- Article in the journal Nature
- This encompasses the first three
- P. D. Gingerich and E. L. Simons. 1977. Systematics, phylogeny, and evolution of early Eocene Adapidae (Mammalia, Primates) in North America. Contributions from the Museum of Paleontology, University of Michigan 24(22):245-279
- Systematic analysis of Omomyiform phylogeny
- Henke, Winfried. Tatersall, Ian. Hardt, Thorolf. Handbook of Paleoanthropology: Phylogeny of Hominids, pub. 2007.
- Homo heidelbergensis Click on the link, 'Evolutionary tree'.
- "Modern humans and Neanderthals share a tangled genetic web" - Phys.org