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1.4.16.10: Evolutionary History of Reptiles - Biology

1.4.16.10: Evolutionary History of Reptiles - Biology


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Learning Outcomes

  • Discuss the evolution of reptiles

Reptiles originated approximately 300 million years ago during the Carboniferous period. One of the oldest known amniotes is Casineria, which had both amphibian and reptilian characteristics. One of the earliest undisputed reptiles was Hylonomus. Soon after the first amniotes appeared, they diverged into three groups—synapsids, anapsids, and diapsids—during the Permian period.

The Permian period also saw a second major divergence of diapsid reptiles into archosaurs (predecessors of crocodilians and dinosaurs) and lepidosaurs (predecessors of snakes and lizards). These groups remained inconspicuous until the Triassic period, when the archosaurs became the dominant terrestrial group due to the extinction of large-bodied anapsids and synapsids during the Permian-Triassic extinction. About 250 million years ago, archosaurs radiated into the dinosaurs and the pterosaurs.

Although they are sometimes mistakenly called dinosaurs, the pterosaurs were distinct from true dinosaurs (Figure 1). Pterosaurs had a number of adaptations that allowed for flight, including hollow bones (birds also exhibit hollow bones, a case of convergent evolution). Their wings were formed by membranes of skin that attached to the long, fourth finger of each arm and extended along the body to the legs.

The dinosaurs were a diverse group of terrestrial reptiles with more than 1,000 species identified to date. Paleontologists continue to discover new species of dinosaurs. Some dinosaurs were quadrupeds (Figure 2); others were bipeds. Some were carnivorous, whereas others were herbivorous. Dinosaurs laid eggs, and a number of nests containing fossilized eggs have been found. It is not known whether dinosaurs were endotherms or ectotherms. However, given that modern birds are endothermic, the dinosaurs that served as ancestors to birds likely were endothermic as well. Some fossil evidence exists for dinosaurian parental care, and comparative biology supports this hypothesis since the archosaur birds and crocodilians display parental care.

Dinosaurs dominated the Mesozoic Era, which was known as the “age of reptiles.” The dominance of dinosaurs lasted until the end of the Cretaceous, the last period of the Mesozoic Era. The Cretaceous-Tertiary extinction resulted in the loss of most of the large-bodied animals of the Mesozoic Era. Birds are the only living descendants of one of the major clades of dinosaurs.

Visit this site to see a video discussing the hypothesis that an asteroid caused the Cretaceous-Triassic (KT) extinction.

Origin of Reptiles

Reptiles evolved from amphibians of Carboniferous period, which depended on water bodies for laying eggs and development of larval stages and hence could not exploit arid habitats far away from water bodies. They invented a large yolk-laden shelled egg that could be laid on land and in which an amniotic sac contained fluid in which embryo could develop to an advanced stage, capable of fending for itself when hatched. The following anatomical changes transformed the ancestral amphibians into land adapted reptiles:

  • Body developed a covering of epidermal scales to prevent loss of body moisture, and skin glands were lost.
  • Skull became monocondylic for better movement and flexibility. Atlas and axis vertebrae together permitted skull movement in all directions.
  • Limb bones and girdles became stronger but limbs were attached on the sides of body, and belly touched the ground during creeping mode of locomotion.
  • Sacral region involved two strong and fused vertebrae to support the body weight on hind legs.
  • Pentadactyle limbs developed claws that helped in climbing on rocks and trees.
  • Lung respiration became more efficient.
  • As a water conservation strategy, metanephros kidneys excreted uric acid which did not require water for excretion.
  • Reptiles continued to be ectothermal since ventricle was not completely partitioned by a septum and blood mixed in heart.
  • Internal fertilization evolved as a large cleioid shelled egg was laid on land.
  • Embryonic membranes amnion, allantois and yolk sac evolved to enable embryonic development in arid conditions.

ANCESTORS OF REPTILES

THE COTYLOSAURS

They were the most primitive stem reptiles that evolved from the labyrithodont amphibians (Embolomeri) in Carboniferous period.

Seymoria was a lizard-like animal, with pentadactyle limbs and a short tail. It had homodont labyrinthine teeth on the jaw bones as well as on vomer and palatine bones. Presence of lateral line indicates its amphibious habits. Skull was monocondylic for better movement of head. Seymoria indicates gradual transition from labyrinthodont amphibians to reptiles. Another 5 foot long cotylosaur fossil, Limnoscelis was found in Mexico that had large premaxillary teeth and long tail.

THE PARAPSIDS

They possessed superior temporal vacuity in the skull and were adapted for aquatic mode of life.

Plesiosaurus was marine long-necked, fish-eating animal with 15 metre long fusiform body, short tail and paddle-like limbs modified for swimming. The skull was euryapsid type with a superior temporal vacuity. The fossils are from lower Jurassic (about 180 million years) and they are believed to have become extinct in end-Cretaceous mass extinction.

Ichthyosaurus had fish-like body with fore limbs modified into paddle-like fins and hind limbs disappeared. There was a fleshy dorsal fin too. Caudal fin was large and bilobed. Jaws projected into an elongated snout and teeth were homodont, an adaptation for fish-catching. Skull was parapsid type with additional postfrontal and supratemporal bones behind the eye orbit. Vertebral column became secondarily simplified with amphicoelous vertebrae.

THE SYNAPSIDS

Synapsids split off from the primitive reptilian stock very early in evolution, perhaps in the middle carboniferous period. Synapsids had started developing mammalian characteristics that enabled them to be fleet-footed and active predators. Their legs commenced to move under the body. Heterodont dentition and false palate started developing in pelycosaurs and had been completely formed in therapsids. Two types of synapsids occurred from carboniferous to Permian, namely, the primitive Pelycosaurs and advanced therapsids.

Pelycosaurs are represented by Dimetrodon whose fossils were discovered from North America and Russia from the late Carboniferous to Permian periods. They were primitive reptile-like animals in which limbs had moved under the body but not completely and each limb had 5 digits with claws. Neural spines on the back were excessively long stretching highly vascularized skin between them that formed a fin-like or sail-like structure. They had heterodont dentition with incisors, canines and molars clearly defined but the false palate had not been completely formed.

Therapsids were more advanced and active synapsids which were perhaps endothermic animals with high rate of metabolism. Heterodont dentition with false palate allowed these animals to chew and grind food for quick digestion in the gut so that high metabolic demand of the body could be fulfilled. Jaw muscles were attached to zygomatic arch to make chewing effective. Carnivore therapsids were called Cynodonts (ex. Cynognathus) and herbivores were Dicynodonts.

THE THECODONTS

They evolved from the sauropsid Archosauria, a group of insignificant lizard-like reptiles that survived the Triassic mass extinction. They evolved into bipedal and highly agile predators.

Euperkeria and Ornithosuchus fossils were unearthed from South Africa and Europe. They were about 2 ft long bipedal lizard-like animals with small head but very long tail for balancing while they chased flying insects by rapid running. Endothermy must have evolved in thecodonts to meet the extraordinary energy demands of their predatory life style.

THE SAURISCHIANS

They were dinosaurs with lizard-like pelvic girdle in which ischium and pubis bones radiated away from each other. They were both bipedal and quadrupedal and carnivores as well as herbivores.

THE ORNITHISCHIANS

They were dinosaurs with bird-like pelvic girdle in which ischium and pubis bones were directed towards posterior as found in modern birds. These were also highly diversified carnivores as well as herbivores and both bipedal and quadruped.

THE PTEROSAURIA

They were flying or gliding dinosaurs of Mesozoic that varied in size from sparrow-sized to some species, like Pteranodon, having a wing span of 8 meters. They had pneumatic bones. Last digit of the fore limb was extraordinarily long and served to attach the membranous patagium between fore limb, hind limb and the body. Hind limbs were used for clinging on to the rocks and cliffs and 3 digits of fore limbs also had curved claws, an adaptation for clinging. Their jaws were modified into beak that possessed homodont dentition but Pteranodon did not have teeth.


Biology and Evolutionary History of Mesosaurs, the Oldest Known Aquatic Reptiles

Mesosaurs are among the most amazing extinct animals they are the oldest known reptiles that developed aquatic adaptations, although how terrestrial their ancestors had become remains to be established they are the only known vertebrates from Gondwana at the Early Permian and they are represented by .

Mesosaurs are among the most amazing extinct animals they are the oldest known reptiles that developed aquatic adaptations, although how terrestrial their ancestors had become remains to be established they are the only known vertebrates from Gondwana at the Early Permian and they are represented by thousands of well preserved and almost complete skeletons. Mesosaurs were capable of inhabiting cold and salty water bodies resulting from the drought of an originally large inland sea that extended over what is now South America and Africa.

So far, mesosaurs are the only tetrapods known from a depauperate ecosystem that included pygocephalomorph crustaceans, algal and microbial mats, and the still unidentified producers of the trace fossil Chondrites. Recently, the discovery of well-preserved mesosaur embryos curled as if within an egg, and one pregnant female yielded clues about early amniote reproductive biology. The fact that mesosaurs may have developed extended embryo retention along with the apparent absence of a mineralized egg-shell may explain the large gap in the fossil record of early amniotic eggs for the first 90 million years of their evolution.

More basic remaining gaps in our knowledge of mesosaurs include taxonomic questions. For instance, how many nominal mesosaur taxa are valid? What are the affinities of mesosaurs?

These interesting aspects of mesosaur biology, along with a reappraisal of their diet and aquatic adaptations, as well as the analysis of the taxonomic problems that are still unresolved justify a Research Topic on mesosaurs in Frontiers in Earth Science. The aim of this proposal is to contrast earlier hypotheses about this taxon and contrast it to recent or new hypotheses that stem from the new data produced in the last few years.

We seek contributions from recognized specialists of early amniote evolution, comparative anatomy and reproductive strategies of extant reptiles, and mesosaurs. We believe that this collection of papers will be useful for a wide range of researches, from those working on paleoecology of basal tetrapods to those focusing on various aspects of vertebrate evolution or paleobiology.

Important Note: All contributions to this Research Topic must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. Frontiers reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of peer review.


Definition of Marine Reptiles

It is firstly important to define the phrase “marine reptile.” Each of the two words requires clarification to avoid confusion. First, the word “marine” is restricted to those vertebrates that feed almost exclusively in the sea in this contribution. This is stricter than the more common usage where any vertebrate that spends time at sea at all is included. The restricted usage is preferred here to remove ambiguity. About 250 species of extant reptiles live in haline habitats or occasionally invade them (Wilfred 1958). Extreme examples are large reptiles in the Southeast Asia–Australia, namely the saltwater crocodile (Crocodylus porosus), Asian water monitor (Varanus salvator), and reticulated python (Python reticulatus). They can swim across long distances in the ocean (e.g., Rosenzweig 2001 Borden 2007) and at least the crocodile and monitor lizard may even feed on fish, but they spend most of their time in other places through a year. The saltwater crocodile especially is often considered marine, but it is unclear whether it is more marine than the Asian water monitor, which is seldom called marine. The restricted usage of “marine” in this contribution would remove all of these ambiguous animals from consideration as marine reptiles.

Second, the word “reptile” is restricted to those vertebrates that are called reptiles in common English (i.e., “lizards,” snakes, tuataras, crocodiles, and the fossils related to them). Birds are descendants of some reptiles, so they are reptiles themselves in a strict sense. However, inclusion of birds, which are warm-blooded, would obscure the discussion. I therefore remove birds from “reptiles” in this contribution. In summary, “marine reptiles” in the current context are all reptiles except birds that feed almost exclusively in the sea.


Did adaptive radiations shape reptile evolution?

Animals sampled in the analysis. Colors indicates rates of evolution: warm colors high rates and cool colors low rates Credit: Tiago R. Simões

Some of the most fundamental questions in evolution remain unanswered, such as when and how extremely diverse groups of animals—for example reptiles—first evolved. For seventy-five years, adaptive radiations—the relatively fast evolution of many species from a single common ancestor—have been considered as the major cause of biological diversity, including the origins of major body plans (structural and developmental characteristics that identify a group of animals) and new lineages. However, past research examining these rapid rates of evolution was largely constrained by the methods used and the amount of data available.

In a paper out today in Nature Communications, a research team lead by Harvard University examined the largest available data set of living and extinct major reptile groups (such as marine reptiles, turtles, lizards, and the ancestors of dinosaurs and crocodiles) to tackle the longstanding question of how adaptive radiations have shaped reptile evolution. Using DNA information from modern species and hundreds of anatomical features from both modern and fossil species for statistical analysis, the study detected that periods of fast anatomical change during the origin of reptile groups often predate when those groups diversified into hundreds or thousands of species. This contradicts long-held ideas of adaptive radiation in evolution biology.

"Our findings suggest that the origin of the major reptile groups, both living and extinct, was marked by very fast rates of anatomical change, but that high rates of evolution do not necessarily align with taxonomic diversification" said first author Dr. Tiago Simões, Postdoctoral Fellow in in the lab of Stephanie Pierce, AssociateProfessor in the Department of Organismic and Evolutionary Biology at Harvard University.

Simões and Pierce revealed that rates of evolution and morphological variety in reptiles prior to the Permian-Triassic Mass Extinction—the biggest mass extinction of all time—were equally high, or even higher, than after the event. As reptile species diversity was much lower during the Permian compared to Triassic, these results indicate that fast rates of evolution do not need to coincide with rapid taxonomic diversification as predicted by the classical theory of adaptive radiation. The two can be decoupled.

The team, which also included Ph.D. student Oksana Vernygora and Professor Michael Caldwell at the University of Alberta, further discovered that accelerated rates of evolution correspond to the origin of unique reptile body plans, but that very similar functional adaptations in reptiles can arise through varying rates of evolution.

"Surprisingly," Pierce said, "reptiles that evolved similar protective armour like turtles or serpentine bodies like snakes, show radically different rates of evolution, indicating the origin and evolution of unique body plans is heterogeneous through evolution."

"Our results also show that the origin of snakes is characterized by the fastest rates of anatomical change in the history of reptile evolution," said Simões. "But, that this does not coincide with increases in taxonomic diversity [as predicted by adaptive radiations] or high rates of molecular evolution."

The mismatch between morphological and molecular evolution supports the idea that protein coding DNA sequences do not seem to be correlated with broad-scale changes in anatomy. Although much more research is needed to understand how body plans evolve, the team hypothesizes that non-protein coding regions of the genome may be responsible for rapid morphological change, as these parts are more free to mutate and take on new functional roles.

"It is clear to us that to advance our understanding of the major patterns in evolution we need further studies capable of measuring phenotypic and molecular evolutionary rates, times of origin, and phenotypic diversity across large timescales" said Simões.

Simões and colleagues continue to develop new methods and are expanding their data set back in time to look at the origins of amniotes, the group that includes both reptilesand mammals. Of particular interest is pinpointing when in geological time these two groups of animals diverged and how extinction, diversification, and adaptation have shaped their evolutionary history over the last 300+ million years.

"I'm excited to continue my research to unravel the early evolutionary dynamics of the two most successful groups of animals on the planet," Simões said. "I'm also focusing on improving available protocols to analyze morphological data and construct more robust evolutionary trees, including the timing of origin of major vertebrate lineages."


References

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Baxter S. 2003. Revolutions in the earth: James Hutton and the true age of the world. Weidenfeld & Nicolson, London.

Bowler P.J. 1989. Evolution: The history of an idea. University of California Press, Berkeley.

Browne E.J. 1996, 2002 (2 volumes). Charles Darwin: A biography. Princeton University Press, Princeton, New Jersey.

Browne E.J. 1995. Charles Darwin: Voyaging, Volume 1 of a Biography. Jonathan Cape, London.

Browne E.J. 2002. Charles Darwin: The power of place. Jonathan Cape, London.

Buckland W. 1824. Notice on the Megalosaurus or great fossil lizard of Stonesfield. Trans. Geolog. Soc. A (Series 2), 1: 390&ndash396.

Bumpus H.C. 1899. The elimination of the unfit as illustrated by the introduced sparrow, Passer domesticus. Biol. Lectures, Marine Biol. Lab, Woods Hole: 209&ndash226.

Carlson E.A. 2004. Mendel&rsquos legacy: The origin of classical genetics. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.

Chambers N. 2000. The letters of Sir Joseph Banks. Imperial College Press, London.

Chambers R. 1844 (reprinted 1994). Vestiges of the natural history of Creation (1st edition reprinted in James Secord, ed, Chicago). University of Chicago Press, Chicago.

Darwin C. 1839. Journal of researches into the geology and natural history of the various countries visited by H.M.S. Beagle, under the command of Captain FitzRoy, R.N., from 1832 to 1836. Henry Colburn, London.

Darwin C. and Wallace A.R. 1858. On the tendency of species to form varieties and on the perpetuation of varieties and species by natural means of selection. Proc. Linn. Soc. (Zool.) 3: 45&ndash62.

Desmond A. and Moore J.R. 1991. Darwin (2 volumes). Michael Joseph, London Viking Penguin, New York.

Fisher R.A. 1918. The correlation between relatives on the supposition of Mendelian inheritance. Proc. R. Soc. Edinburgh 52: 399&ndash433.

Hamilton W.D. 1996. Narrow roads of gene land, Volume 1: Evolution of social behaviour. W.H. Freeman, Oxford.

Hill W.G. 1984. Quantitative genetics, Part 1 (Benchmark Papers in Genetics). Van Nostrand Reinhold International, New York.

Hutton J. 1794. An investigation of the principles of knowledge and of the progress of reason, from sense to science and philosophy, Vol. 2. Strahan and Cadell, Edinburgh.

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Introduction

Squamate venoms are complex mixtures of protein and peptide components (commonly referred to as toxins) that act to kill or immobilise prey, and may possibly aid in digestion. The origin of the venom apparatus of squamates has been the subject of considerable recent research interest. The homology of the venom apparatus across the advanced snakes (Caenophidia) is robustly supported by anatomical evidence 1,2,3,4 , as well as comparative embryology and developmental genetics 5 . A recent addition to the body of evidence supporting the single early evolution of venom in snakes has been the use of protein amino acid or DNA gene sequences from toxins, and their homologues among non-venom body proteins 6,7 . Venom toxins belong to multiple multi-locus gene families, evolving according to the birth and death model 8 , and first acquired their role within venom following recruitment from protein families fulfilling ordinary physiological functions 9 . Mapping the gene tree of these protein families onto the corresponding organismal tree allows the reconstruction of the history of the recruitment of the toxin into the venomous arsenal of the animals. This approach provided additional support for the single early evolution of venom in the Caenophidia 7 .

Among lizards, only the genus Heloderma (family Helodermatidae) was considered to be venomous until very recently. As the venom apparatus of Heloderma is confined to the lower jaw, whereas that of snakes is restricted to the upper jaw, the two systems had always been assumed to be non-homologous. However, this assumption was challenged by Fry et al. 10 , who identified toxin-secreting glands in the lower jaws of additional lizards of the families Varanidae and Anguidae, and in both upper and lower jaws of representatives of the Iguania. As these three groups, together with the Helodermatidae and Serpentes (snakes), form a monophyletic group, Fry et al. 10 postulated a single early origin (SEO) of venom at the base of that clade, termed the Toxicofera (see Supplementary Fig. S1 for a phylogeny of the Toxicoferan reptiles). However, in the absence of strong morphological or developmental evidence of homology between the upper jaw glands of iguanian lizards and snakes, the key piece of evidence for the single origin of venom rested with toxin gene phylogenies, which showed the monophyly of lizard and snake toxin genes to the exclusion of non-venom homologues, and in some cases the lack of reciprocal monophyly of snake and lizard toxins 10 .

The major problem with the interpretation of these gene phylogenies is the lack of comparable sequences of non-venom homologues from within the Toxicofera. In the absence of available genomic sequences, non-toxin homologues of the venom toxins in these studies were derived from a variety of other vertebrate taxa, most commonly mammals or birds 7,9,10,11,12 . This is potentially problematic, because failure to sample non-toxin homologues from the focal clade can lead to gene trees that falsely depict the toxin genes as monophyletic, leading to the erroneous conclusion that they are the result of a single recruitment event (Fig. 1a,b) The rigorous testing of toxin monophyly in any protein family therefore requires the inclusion of non-toxin homologues from within the focal clade (Fig. 1c).

Diagram showing the potential effect of sampling non-venom proteins from in-group taxa on the interpretation of toxin recruitment. (a) Actual gene family evolution within organismal phylogeny (b) effect of non-inclusion of non-toxin sequences: gene tree suggests single early recruitment of toxin genes into venom (c) sampling of non-toxin sequences from in-group reveals non-monophyly of toxins, suggesting multiple independent recruitment events.

Two additional key assumptions that have remained untested due to the lack of non-toxin homologues from previous studies are that changes of role from physiological function into venom are rare in protein family evolution, and that there is no 'reverse recruitment' of toxin proteins back into a physiological role. Consequently, the current narrative of venom evolution rests on two key assumptions that have remained untested, again largely due to the lack of available in-group, non-toxin sequences.

Recently, Toxicoferan non-toxin sequences have become available, thanks to transcriptomic studies involving multiple organs of one Caenophidian (Thamnophis elegans 13 ), and heart and liver tissue from a basal snake (Python bivittatus, as P. molurus bivittatus 14 ). Here, we use these new sequences of physiological proteins sourced from non-venom gland tissues to rigorously test the hypothesis of an early recruitment of nine toxin families into the venom arsenal of squamate reptiles. Evidence of toxin monophyly following the inclusion of sampled non-toxin gene homologues will provide strong support for the SEO hypothesis proposed by Fry et al. 10 In contrast, evidence of toxin non-monophyly (that is, non-toxins nesting within toxin clades) would indicate that either multiple origins of venom have occurred in the squamate reptiles or that the recruitment of proteins into the venom gland may not be a one-way process, but also involve reverse recruitment of toxins into non-venom functions outside the venom gland. To explicitly test these hypotheses, we utilised rigorous phylogenetic analyses alongside ancestral character state reconstructions to investigate the origin of venom, and the nature and frequency of recruitments into and from a toxin function in squamate venom protein families.


Leache Lab

Dr. Leonard Jones successfully defended his dissertation! His presentation was outstanding: “Exploring snake evolution through time and space“. He did a great job of presenting his dissertation chapters on populations genetics, phylogeography, and phylogenomics — all with examples in snakes. Dr. Jones plans to continue his research on snakes as he acquires new skills during his upcoming postdoctoral position at Michigan State University in the Bradburd lab.

Western Fence Lizards @Puget Sound

Western Fence Lizards (Sceloporus occidentalis) are super abundant and common lizards throughout their range in the Western USA. They are found from sea level to high elevations in the Sierra Nevada Mountains, and they are even adapted to live in urban environments. Here in Western Washington, the story is quite different. They seem to be really picky about where they will live , and you can mostly only find them at pristine coastline habitats around the Puget Sound and Hood Canal that are south-facing where they can get a lot of sun exposure. They probably had a much broader distribution in the past, but development of coastlines seems to have wiped out a lot of suitable habitat. The populations that we find today are highly fragmented and scattered around the tiny bits of beaches that are still available. There are very few historical records for these lizards in museum collections from this region, but a couple of important specimens are from places that are completely urbanized with no sign of lizards today (like downtown Seattle). This suggests that more habitats used to be available, even though they are gone today.

A Western Fence Lizard enjoying a sunny day on the beach in the Puget Sound, Ketron Island.

Congratulations Shanelle!

Congratulations to undergraduate researcher Shanelle Wikramanayake on her recent graduation from UW! Shanelle conducted independent research on the conservation genetics of an endemic lizard in Sri Lanka, the rough-nosed horned lizard (Ceratophora aspera). Shanelle is moving to California to attend graduate school at California State University Northridge where she will work on the evolutionary biology and behavior of red-eyed tree frogs with Dr. Jeanne Roberston. We already miss Shanelle in Seattle, but we’re also excited for her future work in her new lab!

Shanelle featured on the announcement for the 2019 UW Undergraduate Research Symposium

Reptile & amphibian illustrations

Simone Des Roches, a herpetologist and Postdoctoral Fellow in the UW School of Aquatic and Fisheries Sciences, was recently featured in a Burke Museum Q&A about her biological illustration work. Simone is producing a series of biological illustrations depicting the reptiles and amphbians of Washington State. The illustrations focus on presenting the diversity found within each species. You can read the full story and see more of the illustrations here:
https://www.burkemuseum.org/news/qa-biological-illustrator

An example of Simone’s illustrations showing geographic variation in Western Fence Lizards (Sceloporus occidentalis).

Frog conservation work

Recent lab graduate Itzue Caviedes-Solis recently published a new research article on frog conservation in the Mexican Highlands. The research was picked up by “Cientificas Mexicanas” and turned into a really nice infographic.


World’s ‘Smallest Dinosaur’ Revealed to Be a Mystery Reptile

The amber-encased fossil was touted as the smallest fossil dinosaur ever found. Known from little more than a peculiar skull, and described early in 2020, Oculudentavis khaungraae was presented as a hummingbird-sized toothed bird—an avian dinosaur that fluttered around prehistoric Myanmar about 100 million years ago. But from the time this Cretaceous creature appeared in the pages of Nature, debate and controversy have circled this strange fossil and its identity. And today, in a peer-reviewed paper published in Current Biology, scientists have confirmed this small creature was no bird at all.

The original Oculudentavis fossil is preserved in a chunk of amber from the southeast Asian country of Myanmar. When it was presented in Nature in March of 2020, outside researchers quickly pointed out that Oculudentavis was not really a bird. The fossil seemed to represent a small reptile that simply resembled a bird thanks to a large eye opening in the skull and a narrow, almost beak-like snout. The original Nature paper was retracted and a reanalysis of the paper’s dataset by another team supported the idea that the fossil wasn’t a bird. A second specimen soon turned up and appeared in a pre-print the same year, adding evidence that these fossils were far from the avian perch on the tree of life. That study has since evolved into the Current Biology paper on what Oculudentavis might be, and it suggests that this bird was really a lizard.

How could a little reptile be mistaken for a bird in the first place? There are several factors that played into the confusion, says lead author and University of Bristol paleontologist Arnau Bolet. “The long and tapering snout and the vaulted skull roof gave the first fossil the overall appearance of a bird-like creature,” Bolet says. But a closer examination of the fossil, Bolet notes, showed many lizard-like traits not present in birds. The teeth of Oculudentavis are fused to the jaw, for example, which is a trait seen in lizards and snakes. And the shape and connections between particular skull bones in the fossil are seen in lizard-like reptiles and not birds. The discovery of a second possible Oculudentavis fossil helped confirm the conclusion.

Organisms preserved in amber are difficult to study from the outside, but the team created CT scans of the reptile inside the second specimen and also reanalyzed the scans from the original specimen. The second fossil differs in some ways from the first, and so Bolet and colleagues gave the second, slightly-smushed fossil a new name—Oculudentavis naga, named after the Naga people who live in the vicinity of Myanmar’s amber mines. There are enough differences between the skull bones of the two fossils that there seem to have been at least two Oculudentavis species, the researchers propose, both representing some mysterious form of lizard. Then again, outside experts like Michael Caldwell of the University of Alberta suggest, Oculudentavis might not be a lizard at all but something much more ancient and unusual.

The amber preserved part of Oculudentavis naga includes its skull, scales and soft tissue. (Adolf Peretti / Peretti Museum Foundation)

Despite its use in common language, “lizard” doesn’t mean just any sprawling reptile with four legs. The modern tuatara, for example, looks like a lizard but actually belongs to a different evolutionary group that last shared a common ancestor with lizards more than 250 million years ago. A lizard, more specifically defined, belongs to a particular group of reptiles called squamates that also includes snakes and “worm lizards.”

“What is this thing? I think it remains an open question,” Caldwell says.

In the new study, the authors used several different comparative techniques to determine how Oculudentavis relates to other lizards. But none of the attempts provided a consistent answer. In some hypothetical evolutionary trees, for example, Oculudentavis seems to be one of the earliest lizards, while in others it seems to be related to the ancestors of the seagoing mosasaurs that thrived during the Cretaceous. “Although Oculudentavis has many peculiarities that make it a weird lizard, facing difficulties in working out the affinities of a fossil lizard to a specific group of lizards is not unusual,” Bolet says, noting that the possible discovery of more fossils with parts of the skeleton other than the head might help.

Paleontologists as yet know little of the lizards and other reptiles that were around during this time. “Oculudentavis comes from amber deposits about 98 million years old,” says University of Bristol paleontologist Jorge Herrera Flores, “and, so far, the fossil record of terrestrial squamates of that age were extremely rare and scarce.” The Oculudentavis fossils not only help fill that gap, but suggest that there is much more to be found. After all, Herrera Flores points out, there are over 10,000 species of squamates on the planet right now. Even accounting for how difficult it can be for small animals to become part of the fossil record, there are undoubtedly many new finds that will help paleontologists better understand the world of small reptiles in the Age of Dinosaurs.

Efforts to find more fossils like Oculudentavis, however, are complicated by the “blood amber” market that often brings these fossils to the attention of researchers. The mines where Cretaceous amber fossils are found are controlled by the Myanmar military, which seized control of the country earlier this year and for years has committed acts of genocide against the country’s Muslim Rohingya people, among others. High-priced sales of amber specimens have fueled the conflict, and even ethically-sourced fossils often end up in the hands of private dealers who restrict access to researchers and stall efforts to re-investigate previous results.

The uncertainty around Oculudentavis makes sense given how odd the fossils look even at a glance, especially compared to other lizards that have been found in amber from around the same place and time. “I think these two things are really interesting,” Caldwell says, “not because they’re birds and not because they’re lizards, but because they’re some kind of proto-lizard things.”

The isolated location of prehistoric Myanmar might explain why such a confounding creature evolved in the first place. During the time Oculudentavis was climbing around, what’s now Myanmar was a piece of land that split off from other landmasses. The area was encapsulated as an island, isolated in the ancient sea, and such places often act as refuges where ancient lineages evolve in isolation. “From what I can see from the vertebrate remains,” Caldwell says, “some very unique things are there and have really ancient ancestry.”

CT imaging allowed researchers to examine each feature of Oculudentavis naga at high resolution without damaging or destroying the specimen. (Edward Stanley / Peretti Museum Foundation)

What role the Oculudentavis species played in their ecosystem is another puzzle. The shape of the jaws and tiny teeth, Bolet says, hint that this reptile snatched insects. Perhaps this creature climbed through ancient forests, looking for invertebrate morsels to eat. Likewise, says study co-author Susan Evans, “there is also some evidence from the skin folds under the head that these animals used them for some form of display,” similar to anole lizards today.

Rather than coming to a neat conclusion, the story of Oculudentavis has raised additional questions. If this reptile really was a lizard, what kind is it? And why is it so different? And if it’s not a lizard, what evolutionary story does the fossil tell? The strange traits in these two specimens might hint that they represent an evolutionary branch that goes off deep into the prehistoric past, one that experts are only beginning to become aware of.

About Riley Black

Riley Black is a freelance science writer specializing in evolution, paleontology and natural history who blogs regularly for Scientific American.


What can we learn about our limbs from the limbless?

November, 2015
By guest authors Christopher A. Emerling, PhD, NSF Postdoctoral Fellow, UC Berkeley Museum of Vertebrate Zoology and Stephanie Keep, Editor of Reports of the National Center for Science Education, and science curriculum consultant for Keep Learning, LLC

"The amniote phallus and limbs differ dramatically in their morphologies…" So begins a recent study published in the journal Developmental Cell. Though you can no-doubt easily distinguish a leg from a penis, it turns out that these functionally distinct appendages share similar genetic pathways. Scientists made this discovery in a surprising way &mdash by examining the genomes of various snake species. Snakes do not have limbs, of course, so how could they have been the key to an insight about limb development?

Where's the evolution?

Snakes originated at least 100 million years ago. Some experts contend that snakes evolved on land and lost their limbs &mdash first the forelimbs, then the hindlimbs &mdash as they adapted to a burrowing lifestyle. Others prefer the hypothesis that they evolved from a group of aquatic reptiles, and lost their limbs as they adapted to the sea. Either way, snakes probably descended from a lineage of fully legged lizards based on three general lines of evidence. First, snakes are genetically nested deep within the lizard clade (Squamata). Second, the fossil record of snakes includes several species that retained hindlimbs (e.g., Eupodophis, Pachyrhachis), with a recently discovered putative (and controversial!) snake that possessed all four limbs (Tetrapodophis). Finally, some of the earlier branches of the snake phylogenetic tree, particularly boas and pythons, include species that possess embryonic hind limb buds that fail to develop into fully formed limbs.

In a previous post, we discussed how genes can be completely deleted from a genome or accumulate inactivating mutations, thereby rendering the gene nonfunctional. You might imagine that the genes encoding limbs were similarly inactivated or lost from the genomes of snakes. In reality, however, there are probably no true "limb genes." Instead, limbs appear to develop based on the contributions of various developmental genes that have multiple functions. Such genes are called pleiotropic, and researchers do not typically expect pleiotropic genes to disappear or become "broken" during evolution since it could have widespread and deleterious effects on an organism's phenotype.

If natural selection prevents animals from losing the genes that are involved in developing appendages, how is it that species like snakes have lost their limbs? One probable pathway is via the disruption of DNA regions known as enhancers. Enhancers are not genes, meaning they do not encode a protein, but they do regulate gene activity. They do this via proteins known as transcription factors, which bind to the enhancers, leading to the transcription of a (usually) nearby gene. Multiple enhancers can be associated with a single gene, and different transcription factors bind to distinct enhancers, controlling when and where the gene is turned on. The regulatory effects of transcription factors and enhancers helps to explain how an entire organism can develop from a single, undifferentiated fertilized egg. As sets of regulatory proteins interact with distinct enhancers, they direct different sets of genes to express themselves in various locations. This allows cells to specialize and differentiate, eventually forming tissues and organs.

If an enhancer were deleted, some functions of a gene may be lost, but enhancers associated with other sets of transcription factors &mdash and therefore other gene functions &mdash would be unaffected. Thus, the researchers were curious: Did snakes lose their limbs because limb-specific enhancers were disrupted during snake evolution? The team examined the genomes of a boa (Boa constrictor), Burmese python (Python bivittatus), and king cobra (Ophiophagus hannah) and compared them to four-legged reptilian relatives such as the American chameleon (Anolis carolinensis) and painted turtle (Chrysemys picta). Though they found some leg enhancers were missing in the genomes of snakes, many were retained, suggesting that they may have functions outside of limb development.

The researchers dove further into this question and discovered that much of the regulatory DNA associated with limb development, including enhancers, overlaps with the genital tubercle, the developmental predecessor to the phallus. They then examined the Tbx4 gene, a transcription factor expressed during formation of the mouse hindlimb and genital tubercle. They confirmed that Tbx4 is expressed in the embryonic hindlimb of the chameleon and the rudimentary hind limbs of the ball python (Python regius), as well as the phalluses of both species and the corn snake (Pantherophis guttatus). Next, they examined HLEB, an enhancer associated with Tbx4. When the researchers transmitted the HLEB enhancer from the chameleon to the mouse, it retained its activity in both the hindlimbs and the genital tubercle, whereas when they transmitted HLEB from the Burmese python and king cobra to the mouse, it lost all hindlimb activity! Together, these data suggest that snakes have retained limb-development genes and the limb-associated enhancers involved in phallus development, though these have evolved in such a way that their limb-development function has been lost.

One of the incredibly useful aspects about evolution is that multiple lineages can independently evolve the same phenotype, allowing for multiple tests of the same hypotheses. As such, understanding how snake genomes evolved to lose their limb-building toolkit can be useful in informing how other lineages lost their limbs. As we have discussed in a previous article, numerous other lineages of lizards have reduced their limbs or eliminated them entirely, including skinks, geckos, and many others. Do these legless lizards show a similar pattern of limb enhancer loss? Or, did they evolve leglessness by another mechanism altogether? Further research is necessary to test these hypotheses.

Among mammals, whales appear to have descended from small hoofed mammals, with the earliest whales having fully intact hind limbs. In most modern species, however, the hindlimbs have disappeared, though some retain a small remnant. Nonetheless, there are multiple recorded examples of individual dolphins with hind flippers, suggesting they may retain some of the genomic toolkit to develop these structures, perhaps including many of the hind limb specific enhancers. By contrast, almost all whales have retained their pelvis bones, though not as the "nonfunctional vestiges" that they are so often portrayed as being. Whale pelvic bones have an important function, and it's one that broadens the hindlimb-phallus connection discovered in snakes: They are attachment sites for the muscles that control movement of the whale's penis. In fact, recent research suggests that the size and shape of these whale pelvic bones may be evolving under sexual selection.

Finally, the caecilians represent a group of amphibians that no longer have legs, and also do not have true phalluses. Though they have a structure with a similar function, true phalluses probably appeared in the lineage that gave rise to mammals, reptiles and birds. In fact, a paper published just within the last week showed that embryos of a very basal lineage of reptiles, the tuatara, have the same phallus precursors as other reptiles, birds and mammals, despite not having a phallus as an adult. Since caecilians independently evolved a phallus and lack limbs, they may provide a better understanding of how the development of limbs and phalluses became intertwined.

So what can we learn about our limbs from the limbless? Quite a bit it turns out, especially in regards to their relation to the penis! By studying the genomes evolution of other lineages of limbless animals, certainly many more answers about limb development can be gleaned.


If birds evolved from dinosaurs, would that make them reptiles too?

Yes, birds are reptiles, but let me explain a bit. Biologists use two types of classification systems, the Linnaean and the phylogenetic. The Linnaean system was developed by Carolus Linnaeus in the 1730's. In the Linnaean system, organisms are grouped by characteristics regardless of their ancestry. So a reptile is an animal that is ectothermic and has scales, and birds would not be reptiles. In the 1940's, a biologist named Willi Hennig came up with another classification system that he called phylogenetics. In this system, organisms are grouped only by their ancestry, and characteristics are only used to discover the ancestry. So a reptile is any animal descended from the original group called reptiles. Both birds and mammals share ancestors sometimes referred to as reptile-like animals (Reptiliomorpha), but it's not very common for people to talk about mammals as reptiles. The situation is different for birds. Birds are part of the group Diapsida, which also includes all other living reptiles (crocodilians, turtles, tuataras, and squamates (mostly snakes and lizards)).

Usually what people mean when they say birds are reptiles is that birds are more closely related to reptiles than anything else, and this is true in a way, but there are many types of reptiles. Birds are most closely related to crocodiles. To understand this, we should look at some history. The first groups of reptile-like animals evolved about 320 million years ago. About 40 million years later, (very quickly by geologic standards), a group called therapsids branched off, which eventually became modern mammals. Other groups of reptiles split off over the next 120 million years, and one branch called the archosaurs were very successful.

Archosaurs were the ancestors of dinosaurs and crocodiles, but they were only distantly related to modern snakes, lizards, and turtles, groups that had split off at different times. Then, 65 million years ago there was a massive extinction event, and all dinosaurs were killed except for a single group of feathered dinosaurs. These evolved over the next 65 million years into modern birds. So birds aren't just closely related to dinosaurs, they really are dinosaurs! And they are most closely related to crocodiles, which also came from archosaurs. This is what most people mean when they say that birds are reptiles, although technically, according to the phylogenetic system, birds, reptiles, and mammals all share a reptile-like ancestor.

You may wonder why biologists have two systems of classification. One reason, of course, is the history behind them, but they are also both useful in their own ways. The phylogenetic system is useful for understanding the relationships between animals, while the Linnaean system is more useful for understanding how animals live. It's sort of like cooking. If you organized all your ingredients phylogenetically, you would put everything that was made from peanuts on the same shelf. Then you could see that peanut butter, peanut oil, and peanut brittle are related to each other. But when you really want to cook, you would use something like the Linnaean system and put all your oils together, all your dry goods together, etc. So both systems have their uses.


Watch the video: ερπετά - αμφίβια -τρίτων (May 2022).


Comments:

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  2. Gunos

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  3. Leigh

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  4. Yolkree

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  5. Mikataur

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