On Pterosaurs and feathers.

Reconstruction of one of the studied anurognathid pterosaurs. Credit: Yuan Zhang/Nature Ecology & Evolution.

Feathers were once considered to be unique avialan structures. Recent studies indicated that non avian dinosaurs, as part of Archosauria, possessed the entirety of the known non keratin protein-coding toolkit for making feathers. Primitive theropods, such as Sinosauropteryx and the tyrannosaurs Dilong and Yutyrannus, and some plant-eating ornithischian dinosaurs, such as Tianyulong and Kulindadromeus, are known from their spectacularly preserved fossils covered in simple, hair-like filaments called ‘protofeathers’.

Other integumentary filaments, termed pycnofibres, has been reported in several pterosaur specimens, but there is still a substantial disagreement regarding their interpretation. J. Yang and colleagues described two specimens of short-tailed pterosaurs (NJU–57003 and CAGS–Z070) from the Middle-Late Jurassic Yanliao Biota, in northeast China (around 165-160 million years ago) with preserved structural fibres (actinofibrils) and four different types of pycnofibres. The specimens resemble Jeholopterus and Dendrorhynchoides, but they are relatively small.


Drawing of of (a) NJU–57003 and (b) CAGS–Z070 with skeletal element identification, outline of
preserved integument, and distribution of the four types of pycnofibres. From Yang et al., 2018.

Types 1 and 4 of pycnofibres occur in both specimens, but types 2 and 3 occur only in CAGS–Z070. This may reflect original biological differences or differences in the taphonomy of the two specimens. The pterosaur type 1 filaments resemble monofilaments in the ornithischian dinosaurs Tianyulong and Psittacosaurus and the coelurosaur Beipiaosaurus. The pterosaur type 2 filaments resemble the brush-like bundles of filaments in the coelurosaurs Epidexipteryx and Yi. Type 3 filaments resemble bristles in modern birds, but surprisingly do not correspond to any reported morphotype in non-avian dinosaurs. The pterosaur type 4 filaments are identical to the radially branched, downy feather-like morphotype found widely in coelurosaurs such as Caudipteryx and Dilong. Functions of these structures could include insulation, tactile sensing, streamlining and colouration (primarily for camouflage and signalling), as for bristles, down feathers and mammalian hairs.

Type 3 filaments (arrows) and similar structures (triangles). Scale bars: 10 mm in a, c and d; 1 mm in b. From Yang et al., 2018

Pterosaurs were winged cousins of the dinosaurs and lived from around 200 million years ago to 66 million years ago. In the early 1800’s, a fuzzy integument was first reported from the holotype of Scaphognathus crassirostris. A recent study on this specimen shows a subset of pycnofibers and actinofibrils. The discovery of integumentary structures in other pterosaurs, such as Pterorhynchus wellnhoferi (another rhamphorhynchoid pterosaur), and these exquisitely preserved pterosaurs from China, suggest that all Avemetatarsalia (the wide clade that includes dinosaurs, pterosaurs and close relatives) were ancestrally feathered.


Yang Z. et al., 2018. Pterosaur integumentary structure with complex feather-like branching. Nature Ecology and Evolution https://doi.org/10.1038/s41559-018-0728-7

Barrett PM, Evans DC, Campione NE. 2015 Evolution of dinosaur epidermal structures. Biol. Lett. 11: 20150229. http://dx.doi.org/10.1098/rsbl.2015.0229

Kai R.K. Jäger, Helmut Tischlinger, Georg Oleschinski, and P. Martin Sander, Goldfuß was right: Soft part preservation in the Late Jurassic pterosaur Scaphognathus crassirostris revealed by reflectance transformation imaging (RTI) and UV light and the auspicious beginnings of paleo-art, https://doi.org/10.26879/713

Craig B. Lowe, Julia A. Clarke, Allan J. Baker, David Haussler and Scott V. Edwards, Feather Development Genes and Associated Regulatory Innovation Predate the Origin of Dinosauria, Mol Biol Evol (2015) 32 (1): 23-28. doi: 10.1093/molbev/msu309


On the rise of the archosauromorphs

Proterosaurus speneri at Teyler’s Museum.

In the aftermath of the devastating Permo-Triassic mass extinction (~252 Ma), synapsid groups such as anomodonts and gorgonopsians and parareptiles such as pareiasaurs, were decimated and largely displaced by the archosauromorphs. The group, which include the ‘ruling reptiles’ (crocodylians, pterosaurs, dinosaurs, and their descendants, birds), originated during the middle–late Permian. The most basal archosauromorphs are Aenigmastropheus and Protorosaurus.

During the Triassic, the archosauromorphs achieved high morphological diversity, including aquatic or semi aquatic forms, highly specialized herbivores, massive predators, armoured crocodile-like forms, and gracile dinosaur precursors. The group constitutes an excellent empirical case to shed light on the recovery of terrestrial faunas after a mass extinction.

The Permian-Triassic boundary at Meishan, China (Photo: Shuzhong Shen)

The massive volcanic eruptions in Siberia at the end of the Permian, covered more than 2 millions of km 2 with lava flows, releasing more carbon in the atmosphere. High amounts of fluorine and chlorine increased the climatic instability, which means that the Mesozoic began under extreme hothouse conditions. Isotope studies and fossil record, indicates that temperatures in Pangaea interiors during the Early Triassic oscillated between 30 and 40 degrees Celsius, with heat peaks in the Induan and during the Early and Late Olenekian. It was suggested that during that time there was a moderate oxygen depletion that caused the low body size of the amphibian and reptilian life-forms found in those rocks.

After the mass extinction event, a distributed archosauromorph ‘disaster fauna’ dominated by proterosuchids, established for a short time. In South Africa, Proterosuchus occurs only between 5 and 14 m above the PT boundary and a similar pattern has been documented for the synapsid Lystrosaurus. During the Olenekian (1–5 million years after the extinction), archosauromorphs underwent a major phylogenetic diversification with the origins or initial diversification of major clades such as rhynchosaurs, archosaurs, erythrosuchids and tanystropheids.

Stenaulorhynchus stockleyi, a rhynchosaur from the Middle Triassic (From Wikimedia Commons)

The Mid Triassic is marked by the return of conifer-dominated forests, and the end of an interval of intense carbon perturbations, suggesting the recovery and stabilization of global ecosystems. The Anisian (5–10 Myr after the extinction) is characterized by a high diversity among the archosauromorphs with the appearance of large hypercarnivores, bizarre and highly specialized herbivores, long-necked marine predators, and gracile and agile dinosauromorphs. This phylogenetic diversity of archosauromorphs by the Middle Triassic paved the way for the ongoing diversification of the group (including the origins of dinosaurs, crocodylomorphs, and pterosaurs) in the Late Triassic, and their dominance of terrestrial ecosystems for the next 170 million years.




Ezcurra MD, Butler RJ. 2018 The rise of the ruling reptiles and ecosystem recovery from the Permo-Triassic mass
extinction. Proc. R. Soc. B 285: 20180361. http://dx.doi.org/10.1098/rspb.2018.0361

Ezcurra MD. (2016) The phylogenetic relationships of basal archosauromorphs, with an emphasis on the systematics of proterosuchian archosauriforms. PeerJ 4:e1778 https://doi.org/10.7717/peerj.1778

Holz, M., Mesozoic paleogeography and paleoclimates – a discussion of the diverse greenhouse and hothouse conditions of an alien world, Journal of South American Earth Sciences (2015), doi: 10.1016/j.jsames.2015.01.001

Molecular signatures of fossil leaves

Leaves of Ptilophyllum mueller, from Emmaville, New South Wales. Scale bars=10 mm (From McLoughlin et al., 2011)

The first plants colonized land approximately 450 million years ago. The transition from an exclusively aquatic to a terrestrial life style implied the evolution of a new set of morphological and physiological features. The most critical adaptive trait for survival during terrestrialization was the ability to retain water in increasingly dehydrating habitats. Consequently, the capacity to maintain a hydrophobic surface layer, or cuticle, over the surfaces of aerial organs was arguably one of the most important innovations in the history of plant evolution.

Spores, pollen and leaf cuticles, are among the most resilient organic structures in the geological record. These components may retain some phylogenetically unique signals, not only in well-preserved fossils, but also in remains with a high level of diagenetic maturity.

Ginkgo biloba, Eocene fossil leaf from the Tranquille Shale of MacAbee, British Columbia, Canada (From Wikipedia Commons)

Generally, the cuticle is divided into two major structural constituents: cutin and cutan. The fatty acid polyesters which constitute cutin, gives the cuticle considerable resistance to biodegradation. Cutan is a non-ester and non-hydrolyzable matrix of aliphatic compounds linked by ether bonds, which remain after cutin hydrolysis. Additionally, the surface of the cuticle may be covered by various long-chain hydrophobic waxes. All these components  favours the survival of the cuticle in many fossil plants, and can be used to resolve the stratigraphic ranges and relationships of extinct plants.

Data from infrared spectroscopy of modern plant cuticles, have been used successfully to support and clarify the species-level taxonomy of extant plants, for example, in Camellia and angiosperm pollen. Using infrared spectroscopy and statistical analysis, researchers at Lund University, the Swedish Museum of Natural History in Stockholm, and Vilnius University, analysed a selection of fossil Cycadales, Ginkgoales and conifers. The team obtained two major groups in the dendrogram of infrared spectra. One branch unites podocarpacean and araucariacean conifers (excluding the Jurassic Allocladus). A relationship consistent with all modern phylogenetic analyses of gymnosperm. The second branch unites a broad range of gymnosperms. Within this branch, Bennettitales (Otozamites and Pterophyllum) form a well-defined group in association with Ptilozamites and Nilssoniales. This cluster is linked to a group incorporating Cycadales on one sub-branch, and Leptostrobales, Ginkgoales and the putative araucariacean Jurassic conifer Allocladus on a second sub-branch.


Dendrogram based on HCA of infrared absorption spectra of an expanded group of 13 fossil gymnosperm taxa (From Vajda et al., 2017)

Early palaeobotanical studies generally linked Bennettitales to Cycadales, but more recent anatomical studies and cladistic analyses have indicated that Bennettitales are not closely related to Cycadales. By contrast, Bennettitales, Nilssoniales and Ptilozamites are grouped closely. Additionally,  the systematic position of Allocladus within Araucariaceae should be reassessed based on its close association with Ginkgo in the cluster analysis of infrared spectra.


Vivi Vajda, Milda Pucetaite, Stephen McLoughlin, Anders Engdahl, Jimmy Heimdal, Per Uvdal. Molecular signatures of fossil leaves provide unexpected new evidence for extinct plant relationships. Nature Ecology & Evolution, 2017; DOI: 10.1038/s41559-017-0224-5

Stephen McLoughlinRaymond J. Carpenter, and Christian Pott, Ptilophyllum muelleri (Ettingsh.) comb. nov. from the Oligocene of Australia: Last of the Bennettitales?, International Journal of Plant Sciences 2011 172:4574-585, DOI: 10.1086/658920

Liaodactylus primus and the ecological evolution of Pterodactyloidea.

Skull of the newfound species Liaodactylus primus (Credit: Chang-Fu Zhou)

Skull of the newfound species Liaodactylus primus (Credit: Chang-Fu Zhou)

Pterosaurs are an extinct monophyletic clade of ornithodiran archosauromorph reptiles from the Late Triassic to Late Cretaceous. The group achieved high levels of morphologic and taxonomic diversity during the Mesozoic, with more than 150 species recognized so far. During their 149 million year history, the evolution of pterosaurs resulted in a variety of eco-morphological adaptations, as evidenced by differences in skull shape, dentition, neck length, tail length and wing span. Pterosaurs have traditionally been divided into two major groups, “rhamphorhynchoids” and “pterodactyloids”. Rhamphorhynchoids are characterized by a long tail, and short neck and metacarpus. Pterodactyloids have a much larger body size range, an elongated neck and metacarpus, and a relatively short tail. Darwinopterus from the early Late Jurassic of China appear to be a transitionary stage that partially fills the morphological gap between rhamphorhynchoids and pterodactyloids.

Pterodactyloidea, the most species-diverse group of pterosaurs, ruled the sky from Late Jurassic to the end of Cretaceous. Liaodactylus primus, a new specimen, discovered in northeast China’s Liaoning province, documents the only pre-Tithonian (145–152 Ma) pterodactyloid known with a complete skull, shedding new light on the origin of the Ctenochasmatidae, a group of exclusive filter feeders, and the timing of the critical transition from fish-catching to filter-feeding, a major ecological shift in the early history of the pterodactyloid clade. The holotype specimen is a nearly complete skull (133 mm long) and mandibles, with the first two cervical vertebrae preserved in articulation with the skull. The elongation of the rostrum, almost half the length of the skull, is accompanied by a significant increase in the number of marginal teeth, giving a total of 152 teeth in both sides of the upper and lower jaws. The teeth are closely spaced to form a ‘comb dentition’, a filter-feeding specialization.

Pterodaustro guinazui cast (Museo Argentino de Ciencias Naturales)

Pterodaustro guinazui cast (Museo Argentino de Ciencias Naturales)

Liaodactylus is the oldest known ctenochasmatid, predating the previously Tithonian (152 Ma) record (Gnathosaurus and Ctenochasma from Germany) by at least 8–10 Myr . The Ctenochasmatidae, represents a long-ranged clade (160–100 Ma), and the only pterodactyloid clade that crossed the Jurassic-Cretaceous transition. The group includes the Early Cretaceous Pterodaustro from Argentina. Popularly called the ‘flamingo pterosaur’, Pterodaustro represents the most remarkable filter-feeding pterosaur known from the fossil record, with a huge number (more than 1000) of densely spaced ‘teeth’ (elastic bristles) in its lower jaws, for filtering small crustaceans, microscopic plankton or algae from open water along lake shores.

Pterosaurs display an extraordinary eco-morphological disparity in feeding adaptations, expressed in skull, jaws and dentition. The Late Triassic Eopterosauria, the basalmost pterosaur clade, were mainly insectivorous. Jurassic insectivores include the Dimorphodontia, Campylognathoididae and Darwinoptera, whereas the Anurognathidae were the only Jurassic insectivores that survived the Jurassic–Cretaceous transition, but became extinct in the Early Cretaceous. The rise of the ctenochasmatid clade was the first major ecological shift in pterosaur evolution from insectivorous-piscivorous to filter-feeding. During Cretaceous time,  the Eupterodactyloidea, a group of advanced pterodactyloids, engaged in a variety of feeding adaptations, including filter-feeding, fish-eating, carnivory and scavenging, herbivory including frugivory, durophagy and omnivory. The Early Cretaceous tapejarids may have been herbivorous, while the pteranodontids, with large skull but tapering and toothless jaws were suitable for seizing fish in open-water environments. Finally, the Late Cretaceous azhdarchids have been hypothesized as foragers feeding on small animals and carrion in diverse terrestrial environments.

Time-calibrated cladogram showing stratigraphic range, eco-morphological diversity of pterosaur clades. (Adapted from Zhou et al., 2017)

Time-calibrated cladogram showing stratigraphic range, eco-morphological diversity of pterosaur clades. (Adapted from Zhou et al., 2017)


Chang-Fu Zhou, Ke-Qin Gao, Hongyu Yi, Jinzhuang Xue, Quanguo Li, Richard C. Fox, Earliest filter-feeding pterosaur from the Jurassic of China and ecological evolution of Pterodactyloidea, 

Andres, B., Clark, J., & Xu, X. (2014). The earliest pterodactyloid and the origin of the group. Current Biology, 24(9), 1011-1016.

WITTON, M. P., 2010 Pteranodon and beyond: the history of giant pterosaurs from 1870 onwards. In: Moody, R.T.J., Buffetaut, E., Naish, D., Martill, D.M. (Eds.), Dinosaurs and Other Extinct Saurians: A Historical Perspective. Geological Society, London, Special Publications 343, 287–311.


Darwin, Owen and the ‘London specimen’.

Portrait of Charles Darwin painted by George Richmond (1840)

Portrait of Charles Darwin painted by George Richmond (1840)

The Archaeopteryx story began in  the summer of 1861, two years after the publication of the first edition of Darwin’s Origin of Species, when workers in a limestone quarry in Germany discovered the impression of a single 145-million-year-old feather. On August 15, 1861, German paleontologist Hermann von Meyer wrote a letter to the editor of the journal Neues Jahrbuch für Mineralogie, Geologie und Palaeontologie, where he made the first description of the fossil. Later, on September 30, 1861, he wrote a new letter:  “I have inspected the feather from Solenhofen closely from all directions, and that I have come to the conclusion that this is a veritable fossilisation in the lithographic stone that fully corresponds with a birds’ feather. I heard from Mr. Obergerichtsrath Witte, that the almost complete skeleton of a feather-clad animals had been found in the lithographic stone. It is reported to show many differences with living birds. I will publish a report of the feather I inspected, along with a detailed illustration. As a denomination for the animal I consider Archaeopteryx lithographica to be a fitting name”. 

The near complete fossil skeleton found in a Langenaltheim quarry near Solnhofen – with clear impressions of wing and tail feathers –  was examined by Andreas Wagner, director of the Paleontology Collection of the State of Bavaria in Germany. He reached the conclusion that the fossil was a reptile, and gave it the name Griphosaurus. He wrote: “Darwin and his adherents will probably employ the new discovery as an exceedingly welcome occurrence for the justification of their strange views upon the transformations of animals.”

Archaeopteryx lithographica, Archaeopterygidae, Replica of the London specimen; Staatliches Museum für Naturkunde Karlsruhe, Germany. From Wikimedia Commons

Archaeopteryx lithographica, Archaeopterygidae, Replica of the London specimen; Staatliches Museum für Naturkunde Karlsruhe, Germany. From Wikimedia Commons

The fossil was later bought by the British Museum of Natural History in London. Richard Owen, head of the Museum, was the first to describe the fossil and named it Archaeopteryx macrura, arguing that its identity with Meyer’s specimen could not be satisfactorily established (Owen 1862a, p. 33 n.). This fossil is also know as the London specimen. Owen, a fervent opponent of the evolutionary theory of Charles Darwin, was convinced that all animals within each larger systematic group were only variations of a single theme, the ‘ideal archetype’.

Hugh Falconer, a Scottish geologist and paleontologist, saw the Archaeopteryx as a valid “transitional” fossil. At that time, he was in  a dispute with Owen, and pointed out that Owen’s description of the Archaeopteryx had missed some essential elements. On January 3, 1863, he wrote a letter to Darwin about the significance of this fossil:  “It is a much more astounding creature—than has entered into the the conception of the describer—who compares it with the Raptores & Passeres & Gallinaceæ, as a round winged (like the last) `Bird of flight.’ It actually had at least two long free digits to the fore limb—and those digits bearing claws as long and strong as those on the hind leg. Couple this with the long tail—and other odd things,—which I reserve for a jaw—and you will have the sort of misbegotten-bird-creature—the dawn of an oncoming conception `a la Darwin.”

Darwin answered that letter on January 20, 1863, and commented about Owen’s mistake: “Has God demented Owen, as a punishment for his crimes, that he should overlook such a point?. “

Richard Owen stands next to the largest of all moa, Dinornis maximus (now D. novaezealandiae). From Wikimedia Commons.

Richard Owen stands next to the largest of all moa, Dinornis maximus (now D. novaezealandiae). From Wikimedia Commons.

In later editions of The Origin of Species, Darwin mention the Archaeopteryx: “That strange bird, Archaeopteryx, with a long lizardlike tail, bearing a pair of feathers on each joint, and with its wings furnished with two free claws . . . Hardly any recent discovery shows more forcibly than this, how little we as yet know of the former inhabitants of the world.”



MEYER v., H. (1861): Archaeopterix lithographica (Vogel-Feder) und Pterodactylus von Solenhofen. Neues Jahrbuch fur Mineralogie, Geognosie, Geologie und Petrefakten-Kunde. 6: 678-679

Falconer, H. letter of January 3, 1863 to Charles Darwin; The Correspondence of Charles Darwin Vol. 11, edited by F. Furkhardt, DM Porter, S. A Dean, J. R Tophan, and S. Wilmot.  Cambridge University Press, Cambridge, 1999

OWEN, R. (1863): On the Archaeopteryx of von Meyer, with a description of the fossil remains of a long-tailed species, from the lithographic stone of Solenhofen. Philosophical Transactions of the Royal Society of London 153: 33-47

Prothero, D. R.  Evolution: What the Fossils Say and Why it Matters. Columbia University Press, New York, 2007.

Peter Wellnhofer, A short history of research on Archaeopteryx and its relationship with dinosaurs, Geological Society, London, Special Publications, 343:237-250, doi:10.1144/SP343.14, 2010



Darwin Correspondence Project http://www.darwinproject.ac.uk/entry-3899


A brief introduction to the origin of Birds.

Archaeopteryx lithographica, specimen displayed at the Museum für Naturkunde in Berlin. (From Wikimedia Commons)

Archaeopteryx lithographica, specimen displayed at the Museum für Naturkunde in Berlin. (From Wikimedia Commons)

Birds originated from a theropod lineage more than 150 million years ago. Their evolutionary history is one of the most enduring and fascinating debates in paleontology. In recent years, several discovered fossils of theropods and early birds have filled the morphological, functional, and temporal gaps along the line to modern birds. The discovered fossils demonstrate that distinctive bird characteristics such as feathers, flight, endothermic physiology, unique strategies for reproduction and growth, and a novel pulmonary system have a sequential and stepwise transformational pattern, with many arising early in dinosaur evolution, like the unusually crouched hindlimb for bipedal locomotion,the furcula and the “semilunate” carpal that appeared early in the theropod lineage (Allen et al., 2013; Xu et al., 2014).  Also, the discovery of Mahakala – a basal dromaeosaurid dinosaur named for one of the eight protector deities in Tibetan Buddhism – suggests that extreme miniaturization and laterally movable arms necessary for flapping flight are ancestral for paravian theropods. In contrast, a number of basal birds resemble theropods in many features.

Sin título

Sciurumimus (A); the basal coelurosaur Sinosauropteryx (B) with filamentous feathers; the deinonychosaurs Anchiornis (C) and Microraptor (D). Adapted from Xu et al., 2014.

Anatomical features like aspects of egg shape, ornamentation, microstructure, and porosity of living birds trace their origin to the maniraptoran theropods, such as oviraptorosaurs and troodontids. In addition, some preserving brooding postures, are known for four oviraptorosaurs, two troodontids, a dromaeosaur, and one basal bird providing clear evidence for parental care of eggs.

In birds, particularly their forebrains, are expanded relative to body size. The volumetric expansion of the avian endocranium began relatively early in theropod evolution. Archaeopteryx lithographica is volumetrically intermediate between those of more basal theropods and crown birds (Balanoff et al., 2013). The digital brain cast of Archaeopteryx also present an indentation that could be from the wulst, a neurological structure present in living birds used in information processing and motor control with two primary inputs: somatosensory and visual. Birds also exhibit the most advanced vertebrate visual system, with a highly developed ability to distinguish colors over a wide range of wavelengths.

Reconstruction of pulmonary components [cervical air-sac system (green), lung (orange), and abdominal air-sac system (blue)] in the theropod Majungatholus (From Xu et al., 2014)

Reconstruction of pulmonary components [cervical air-sac system (green), lung (orange), and abdominal air-sac system (blue)] in the theropod Majungatholus (From Xu et al., 2014)

Feathers were once considered to be unique avialan structures. The megalosaurus Sciurumimus, the compsognathus Sinosauropteryx, and a few other dinosaurs, document the appearance of primitive feathers. More recent studies indicated that non avian dinosaurs, as part of Archosauria, possessed the entirety of the known non keratin protein-coding toolkit for making feathers (Lowe et al., 2015)

The evolution of flight involved a series of adaptive changes at the morphological and molecular levels,like the fusion and elimination of some bones and the pneumatization of the remaining ones. The extensive skeletal pneumaticity in theropods such as Majungasaurus demonstrates that a complex air-sac system and birdlike respiration evolved in birds’ theropod ancestors. The increased metabolism associated with homeothermy and powered flight requires an efficient gas exchange process during pulmonary ventilation. Moreover, recent anatomical and physiological studies show that alligators, and monitor lizards exhibit respiratory systems and unidirectional breathing akin to those of birds, which indicate that unidirectional breathing is a primitive characteristic of archosaurs or an even more inclusive group with the complex air-sac system evolving later within Archosauria.

The earliest diversification of extant birds (Neornithes) occurred during the Cretaceous period and after the mass extinction event at the Cretaceous-Paleogene (K-Pg) boundary, the Neoaves, the most diverse avian clade, suffered a rapid global expansion and radiation. Today, with more than 10500 living species, birds are the most species-rich class of tetrapod vertebrates.



Xing Xu, Zhonghe Zhou, Robert Dudley, Susan Mackem, Cheng-Ming Chuong, Gregory M. Erickson, David J. Varricchio, An integrative approach to understanding bird origins, Science, Vol. 346 no. 6215, DOI: 10.1126/science.1253293.

Puttick, M. N., Thomas, G. H. and Benton, M. J. (2014), HIGH RATES OF EVOLUTION PRECEDED THE ORIGIN OF BIRDS. Evolution, 68: 1497–1510. doi: 10.1111/evo.12363 A.

H. Turner, D. Pol, J. A. Clarke, G. M. Erickson, M. A. Norell, A basal dromaeosaurid and size evolution preceding avian flight. Science 317, 1378–1381 (2007).pmid: 17823350.

V. Allen, K. T. Bates, Z. Li, J. R. Hutchinson, Linking the evolution of body shape and locomotor biomechanics in bird-line archosaurs. Nature 497, 104–107 (2013). doi: 10.1038/nature12059; pmid: 23615616

A. M. Balanoff, G. S. Bever, T. B. Rowe, M. A. Norell, Evolutionary origins of the avian brain. Nature 501, 93–96 (2013). doi: 10.1038/nature12424; pmid: 23903660

M. S. Y. Lee, A. Cau, D. Naish, G. J. Dyke, Sustained miniaturization and anatomical innovation in the dinosaurian ancestors of birds. Science 345, 562–566 (2014). doi: 10.1126/science.1252243; pmid: 25082702

Craig B. Lowe, Julia A. Clarke, Allan J. Baker, David Haussler and Scott V. Edwards, Feather Development Genes and Associated Regulatory Innovation Predate the Origin of Dinosauria, Mol Biol Evol (2015) 32 (1): 23-28. doi: 10.1093/molbev/msu309

A brief introduction about the origin of Eukaryotes.

Sonderia sp. (a ciliate that preys upon various algae, diatoms, and cyanobacteria). Photo credit: Diana Lipscomb, George Washington University, Washington, D.C.

Sonderia sp. (a ciliate that preys upon various algae, diatoms, and cyanobacteria). Photo credit: Diana Lipscomb, George Washington University, Washington, D.C.

In 1883, the first person to suggested the endosymbiotic nature of eukaryotic cells was the German botanist Andreas Schimper, and in 1926 Russian botanist Konstantin Mereschkowsky and American biologist Ivan Wallin, postulated the idea that symbiosis is the main driving force of evolution in their book “Symbiogenesis and the Origin of Species”. In 1981, American Biologist Lynn Margulis published ”Symbiosis in Cell Evolution” and proposed that the complexity of the eukaryotic cell was assembled over a long time period by symbiotic associations between different kinds of prokaryotes and an amitochondriate protozoa host.

The mosaicism of the eukaryotic genome is challenging. Bacteria, Archaea, and Eukarya share common ancestry but they have very distinctive features. Eukarya are similar to Archaea for some systems like the replication, transcription,and translation apparatuses and to Bacteria for others like metabolism and membrane chemistry (Rochette, 2014), so the different hypotheses are associated with different phylogenomic prediction.

(a) The Serial Endosymbiotic Theory and (b) The Neomuran Hypothesis (from Armstrong 2005)

(a) The Serial Endosymbiotic Theory and (b) The Neomuran Hypothesis (from Armstrong 2005)

All these hypotheses can be classified into three main classes: hypotheses involving endosymbiosis, which argue that components of the eukaryotic cell arose by engulfment of prokaryotic organisms,  hypotheses for autogenous (‘self-birth’) pathways for eukaryotic cell components, and a “ternary” hypotheses suggest that the organism that engulfed the ancestor of mitochondria was itself a chimera of two prokaryotes.
The “hydrogen hypothesis” (Martin and Müller 1998) involves endosymbiosis and implies that ancestral eukaryotic genes are derived from the alphaproteobacterial ancestor of mitochondria and from the methanogenic euryarchaeon that hosted it. The Neomura hypothesis (Cavalier-Smith 2010b) is among the autogenous hypotheses and assumes that Eukarya are the sister group of all Archaea. Finally, a popular ternary hypothesis is the “endokaryotic” hypotheses in which the nucleus derives from an archaeon while the cytoplasm derives from a bacterium (Lake and Rivera 1994).
A recent analysis establishes that there is no phylogenomic support in favor of ternary hypotheses and support that Eukarya branch close to Archaea or basally within them and that some early-mitochondria hypotheses are compatible with current genomic data under certain assumptions (Rochette, 2014).

Cosmarium sp. (desmid) near a Sphagnum sp. leaf (Photo Credit: Marek Mis)

Cosmarium sp. (desmid) near a Sphagnum sp. leaf (Photo Credit: Marek Mis)

It’s possible that the last eukaryotic common ancestor (LECA) had a modern nucleus (Mans et al. 2004), a cytoskeleton based on microtubules and actin (Yutin et al. 2009; Hammesfahr and Kollmar 2012), a complete vesicle and membrane-trafficking system allowing for endocytosis (Dacks et al. 2009; Yutin et al. 2009; De Craene et al. 2012), mitochondria (which are derived alphaproteobacteria; Embley and Martin 2006; Gabaldón and Huynen 2007), a modern cell cycle (Eme et al. 2011), and a sexual cycle (Ramesh et al. 2005)


Nicolas C. Rochette, Céline Brochier-Armanet, and Manolo Gouy, Phylogenomic test of the hypotheses for the evolutionary origin of eukaryotes, Mol. Biol. Evol. 2014 : mst272

Yonas I. Tekle,  Laura Wegener Parfrey, Laura A. Katz, Molecular Data Are Transforming Hypotheses on the Origin and Diversification of Eukaryotes, BioScience(2009),59(6):471 http://dx.doi.org/10.1525/bio.2009.59.6.5