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Tuesday, June 2, 2015

Evolution of tetrapods



From Wikipedia, the free encyclopedia

In Late Devonian vertebrate speciation, descendants of pelagic lobe-finned fish — like Eusthenopteron — exhibited a sequence of adaptations: *Panderichthys, suited to muddy shallows *Tiktaalik with limb-like fins that could take it onto land *Early tetrapods in weed-filled swamps, such as: **Acanthostega, which had feet with eight digits **Ichthyostega with limbs Descendants also included pelagic lobe-finned fish such as coelacanth species.

The evolution of tetrapods began about 395 million years ago in the Devonian Period with the earliest tetrapods derived from neither ray-finned nor lobe-finned fishes.[1] Tetrapods are categorized as a biological superclass, Tetrapoda, which includes all living and extinct amphibians, reptiles, birds, and mammals. While most species today are terrestrial, little evidence supports the idea that any of the earliest tetrapods could move about on land, as their limbs could not have held their midsections off the ground and the known trackways do not indicate they dragged their bellies around. Presumably, the tracks were made by animals walking along the bottoms of shallow bodies of water.[2] The specific aquatic ancestors of the tetrapods, and the process by which land colonization occurred, remain unclear, and are areas of active research and debate among palaeontologists at present.

Amphibians today generally remain semiaquatic, living the first stage of their lives as fish-like tadpoles. Several groups of tetrapods, such as the snakes and cetaceans, have lost some or all of their limbs. In addition, many tetrapods have returned to partially aquatic or fully aquatic lives throughout the history of the group (modern examples of fully aquatic tetrapods include cetaceans and sirenians). The first returns to an aquatic lifestyle may have occurred as early as the Carboniferous Period[3] whereas other returns occurred as recently as the Cenozoic, as in cetaceans, pinnipeds,[4] and several modern amphibians.[5]

The change from a body plan for breathing and navigating in water to a body plan enabling the animal to move on land is one of the most profound evolutionary changes known.[6] It is also one of the best understood, largely thanks to a number of significant transitional fossil finds in the late 20th century combined with improved phylogenetic analysis.[7]

Origin

Evolution of fish

The Devonian period is traditionally known as the "Age of Fish", marking the diversification of numerous extinct and modern major fish groups.[8] Among them were the early bony fishes, who diversified and spread in freshwater and brackish environments at the beginning of the period. The early types resembled their cartilaginous ancestors in many features of their anatomy, including a shark-like tailfin, spiral gut, large pectoral fins stiffened in front by skeletal elements and a largely unossified axial skeleton.[9]
They did, however, have certain traits separating them from cartilaginous fishes, traits that would become pivotal in the evolution of terrestrial forms. With the exception of a pair of spiracles, the gills did not open singly to the exterior as they do in sharks; rather, they were encased in a gill chamber stiffened by membrane bones and covered by a bony operculum, with a single opening to the exterior. The cleithrum bone, forming the posterior margin of the gill chamber, also functioned as anchoring for the pectoral fins. The cartilaginous fishes do not have such an anchoring for the pectoral fins. This allowed for a movable joint at the base of the fins in the early bony fishes, and would later function in a weight bearing structure in tetrapods. As part of the overall armour of rhomboid cosmin scales, the skull had a full cover of dermal bone, constituting a skull roof over the otherwise shark-like cartilaginous inner cranium. Importantly, they also had a swim bladder/lung,[10] a feature lacking in sharks and rays.

Lungs before land

The lung/swim bladder originated as an outgrowth of the gut, forming a gas-filled bladder above the digestive system. In its primitive form, the air bladder was open to the alimentary canal, a condition called physostome and still found in many fish.[11] The primary function is not entirely certain. One consideration is buoyancy. The heavy scale armour of the early bony fishes would certainly weigh the animals down. In cartilaginous fishes, lacking a swim bladder, the open sea sharks need to swim constantly to avoid sinking into the depths, the pectoral fins providing lift.[12] Another factor is oxygen consumption. Ambient oxygen was relatively low in the early Devonian, possibly about half of modern values.[13] Per unit volume, there is much more oxygen in air than in water, and vertebrates are active animals with a high energy requirement compared to invertebrates of similar sizes.[14][15] The Devonian saw increasing oxygen levels which opened up new ecological niches by allowing groups able to exploit the additional oxygen to develop into active, large-bodied animals.[13] Particularly in tropical swampland habitats, atmospheric oxygen is much more stable, and may have prompted a reliance of lungs rather than gills for primary oxygen uptake.[16][17] In the end, both buoyancy and breathing may have been important, and some modern physostome fishes do indeed use their bladders for both.

To function in gas exchange, lungs required a blood supply. In cartilaginous fishes and teleosts, the heart lies low in the body and pumps blood forward through the ventral aorta, which splits up in a series of paired aortic arches, each corresponding to a gill arch.[18] The aortic arches then merge above the gills to form a dorsal aorta supplying the body with oxygenated blood. In lungfishes, bowfin and bichirs, the swim bladder is supplied with blood by paired pulmonary arteries branching off from the hindmost (6th) aortic arch.[19] The same basic pattern is found in the lungfish Protopterus and in terrestrial salamanders, and was probably the pattern found in the tetrapods' immediate ancestors as well as the first tetrapods.[20] In most other bony fishes the swim bladder is supplied with blood by the dorsal aorta.[19]

External and internal nares

The nostrils in most bony fish differ from those of tetrapods. Normally, bony fish have four nares (nasal openings), one naris behind the other on each side. As the fish swims, water flows into the forward pair, across the olfactory tissue, and out through the posterior openings. This is true not only of ray-finned fish but also of the coelacanth, a fish included in the Sarcopterygii, the group that also includes the tetrapods. In contrast, the tetrapods have only one pair of nares externally but also sport a pair of internal nares, called choanae, allowing them to draw air through the nose. Lungfish are also sarcopterygians with internal nostrils, but these are sufficiently different from tetrapod choanae that they have long been recognized as an independent development.[21]

The evolution of the tetrapods' internal nares was hotly debated in the 20th century. The internal nares could be one set of the external ones (usually presumed to be the posterior pair) that have migrated into the mouth, or the internal pair could be a newly evolved structure. To make way for a migration, however, the two tooth-bearing bones of the upper jaw, the maxilla and the premaxilla, would have to separate to let the nostril through and then rejoin; until recently, there was no evidence for a transitional stage, with the two bones disconnected. Such evidence is now available: a small lobe-finned fish called Kenichthys, found in China and dated at around 395 million years old, represents evolution "caught in mid-act", with the maxilla and premaxilla separated and an aperture—the incipient choana—on the lip in between the two bones.[22] Kenichthys is more closely related to tetrapods than is the coelacanth,[23] which has only external nares; it thus represents an intermediate stage in the evolution of the tetrapod condition. The reason for the evolutionary movement of the posterior nostril from the nose to lip, however, is not well understood.

Into the shallows


Devonian fishes, including an early shark Cladoselache, Eusthenopteron and other lobe-finned fishes, and the placoderm Bothriolepis (Joseph Smit, 1905).

The relatives of Kenichthys soon established themselves in the waterways and brackish estuaries and became the most numerous of the bony fishes throughout the Devonian and most of the Carboniferous. The basic anatomy of group is well known thanks to the very detailed work on Eusthenopteron by Erik Jarvik in the second half of the 20th century.[24] The bones of the skull roof were broadly similar to those of early tetrapods and the teeth had an infolding of the enamel similar to that of labyrinthodonts. The paired fins had a build with bones distinctly homologous to the humerus, ulna, and radius in the fore-fins and to the femur, tibia, and fibula in the pelvic fins.[25]

There were a number of families: Rhizodontida, Canowindridae, Elpistostegidae, Megalichthyidae, Osteolepidae and Tristichopteridae.[26] Most were open-water fishes, and some grew to very large sizes; adult specimens are several meters in length.[27] The Rhizodontid Rhizodus is estimated to have grown to 7 meters (23 feet), making it the largest freshwater fish known.[28]

While most of these were open-water fishes, one group, the Elpistostegalians, adapted to life in the shallows. They evolved flat bodies for movement in very shallow water, and the pectoral and pelvic fins took over as the main propulsion organs. Most median fins disappeared, leaving only a protocercal tailfin. Since the shallows were subject to occasional oxygen deficiency, the ability to breath atmospheric air with the swim bladder became increasingly important.[6] The spiracle became large and prominent, enabling these fishes to draw air.

Skull morphology

The tetrapods have their root in the early Devonian tetrapodomorph fish.[29] Primitive tetrapods developed from an osteolepid tetrapodomorph lobe-finned fish (sarcopterygian-crossopterygian), with a two-lobed brain in a flattened skull. The coelacanth group represents marine sarcopterygians that never acquired these shallow-water adaptations.
The sarcopterygians apparently took two different lines of descent and are accordingly separated into two major groups: the Actinistia (including the coelacanths) and the Rhipidistia (which include extinct lines of lobe-finned fishes that evolved into the lungfish and the tetrapodomorphs).

From fins to feet


Stalked fins like those of the bichirs can be used for terrestrial movement

The oldest known tetrapodomorph is Kenichthys from China, dated at around 395 million years old. Two of the earliest tetrapodomorphs, dating from 380 Ma, were Gogonasus and Panderichthys.[30] They had choanae and used their fins as to move through tidal channels and shallow waters choked with dead branches and rotting plants.[31] Their fins could have been used to attach themselves to plants or similar while they were lying in ambush for prey. The universal tetrapod characteristics of front limbs that bend forward from the elbow and hind limbs that bend backward from the knee can plausibly be traced to early tetrapods living in shallow water. Pelvic bone fossils from Tiktaalik shows, if representative for early tetrapods in general, that hind appendages and pelvic-propelled locomotion originated in water before terrestrial adaptations.[32]

Another indication that feet and other tetrapod traits evolved while the animals were still aquatic is how they were feeding. They did not have the modifications of the skull and jaw that allowed them to swallow prey on land. Prey could be caught in the shallows, at the water's edge or on land, but had to be eaten in water where hydrodynamic forces from the expansion of their buccal cavity would force the food into their esophagus.[33]

It has been suggested that the evolution of the tetrapod limb from fins in lobe-finned fishes is related to expression of the HOXD13 gene or the loss of the proteins actinodin 1 and actinodin 2, which are involved in fish fin development.[34][35] Robot simulations suggest that the necessary nervous circuitry for walking evolved from the nerves governing swimming, utilizing the sideways oscillation of the body with the limbs primarily functioning as anchoring points and providing limited thrust.[36] This type of movement, as well as changes to the pectoral girdle a similar to those seen in the fossil record can be induced in bichirs by raising then out of water.[37]

A 2012 study using 3d reconstructions of Ichthyostega concluded that it was incapable of typical quadrupedal gaits. The limbs could not move alternately as they lacked the necessary rotary motion range. In addition, the hind limbs lacked the necessary pelvic musculature for hindlimb-driven land movement. Their most likely method of terrestrial locomotion is that of synchronous "crutching motions", similar to modern mudskippers.[38]

Denizens of the swamp

The first tetrapods probably evolved in coastal and brackish marine environments, and in shallow and swampy freshwater habitats.[39] Formerly, researchers thought the timing was towards the end of the Devonian. In 2010, this belief was challenged by the discovery of the oldest known tetrapod tracks, preserved in marine sediments of the southern coast of Laurasia, now Świętokrzyskie (Holy Cross) Mountains of Poland. They were made during the Eifelian stage at the end of the Middle Devonian. The tracks, some of which show digits, date to about 395 million years ago—18 million years earlier than the oldest known tetrapod body fossils.[40] Additionally, the tracks show that the animal was capable of thrusting its arms and legs forward, a type of motion that would have been impossible in tetrapodomorph fish like Tiktaalik. The animal that produced the tracks is estimated to have been up to 2.5 metres (8.2 ft) long with footpads up to 26 centimetres (10 in) wide, although most tracks are only 15 centimetres (5.9 in) wide.[41] The new finds suggest that the first tetrapods may have lived as opportunists on the tidal flats, feeding on marine animals that were washed up or stranded by the tide.[40] Currently, however, fish are stranded in significant numbers only at certain times of year, as in alewife spawning season; such strandings could not provide a significant supply of food for predators. There is no reason to suppose that Devonian fish were less prudent than those of today.[42] According to Melina Hale of University of Chicago, not all ancient trackways are necessarily made by early tetrapods, but could also be created by relatives of the tetrapods who used their fleshy appendages in a similar substrate-based locomotion.[43][44]

Palaeozoic tetrapods

Devonian tetrapods

Research by Jennifer A. Clack and her colleagues showed that the very earliest tetrapods, animals similar to Acanthostega, were wholly aquatic and quite unsuited to life on land. This is in contrast to the earlier view that fish had first invaded the land — either in search of prey (like modern mudskippers) or to find water when the pond they lived in dried out — and later evolved legs, lungs, etc.

By the late Devonian, land plants had stabilized freshwater habitats, allowing the first wetland ecosystems to develop, with increasingly complex food webs that afforded new opportunities. Freshwater habitats were not the only places to find water filled with organic matter and choked with plants with dense vegetation near the water's edge. Swampy habitats like shallow wetlands, coastal lagoons and large brackish river deltas also existed at this time, and there is much to suggest that this is the kind of environment in which the tetrapods evolved. Early fossil tetrapods have been found in marine sediments, and because fossils of primitive tetrapods in general are found scattered all around the world, they must have spread by following the coastal lines — they could not have lived in freshwater only.

One analysis from the University of Oregon suggests no evidence for the "shrinking waterhole" theory - transitional fossils are not associated with evidence of shrinking puddles or ponds - and indicates that such animals would probably not have survived short treks between depleted waterholes.[45] The new theory suggests instead that proto-lungs and proto-limbs were useful adaptations to negotiate the environment in humid, wooded floodplains.[46]

The Devonian tetrapods went through two major bottlenecks during what is known as the Late Devonian extinction; one at the end of the Frasnian stage, and one twice as large at the end of the following Famennian stage. These events of extinctions led to the disappearance of primitive tetrapods with fish-like features like Ichthyostega and their primary more aquatic relatives.[47] When tetrapods reappear in the fossil record again after the Devonian extinctions, the adult forms are all fully adapted to a terrestrial existence, with later species secondary adapted to an aquatic lifestyle.[48]

Excretion in tetrapods

The common ancestor of all present gnathostomes lived in freshwater, and later migrated back to the sea. To deal with the much higher salinity in sea water, they evolved the ability to turn the nitrogen waste product ammonia into harmless urea, storing it in the body to give the blood the same osmolarity as the sea water without poisoning the organism. This is the system currently found in cartilaginous fishes. Ray-finned fishes (Actinopterygii) later returned to freshwater and lost this ability, while the fleshy-finned fishes (Sarcopterygii) retained it. Since the blood of ray-finned fishes contains more salt than freshwater, they could simply get rid of ammonia through their gills.
When they finally returned to the sea again, they did not recover their old trick of turning ammonia to urea, and they had to evolve salt excreting glands instead. Lungfishes do the same when they are living in water, making ammonia and no urea, but when the water dries up and they are forced to burrow down in the mud, they switch to urea production. Like cartilaginous fishes, the coelacanth can store urea in its blood, as can the only known amphibians that can live for long periods of time in salt water (the toad Bufo marinus and the frog Rana cancrivora). These are traits they have inherited from their ancestors.

If early tetrapods lived in freshwater, and if they lost the ability to produce urea and used ammonia only, they would have to evolve it from scratch again later. Not a single species of all the ray-finned fishes living today has been able to do that, so it is not likely the tetrapods would have done so either. Terrestrial animals that can only produce ammonia would have to drink constantly, making a life on land impossible (a few exceptions exist, as some terrestrial woodlice can excrete their nitrogenous waste as ammonia gas). This probably also was a problem at the start when the tetrapods started to spend time out of water, but eventually the urea system would dominate completely. Because of this it is not likely they emerged in freshwater (unless they first migrated into freshwater habitats and then migrated onto land so shortly after that they still retained the ability to make urea), although some species never left, or returned to, the water could of course have adapted to freshwater lakes and rivers.

Lungs

It is now clear that the common ancestor of the bony fishes (Osteichthyes) had a primitive air-breathing lung—later evolved into a swim bladder in most actinopterygians (ray-finned fishes). This suggests that crossopterygians evolved in warm shallow waters, using their simple lung when the oxygen level in the water became too low.

Fleshy lobe-fins supported on bones rather than ray-stiffened fins seem to have been an ancestral trait of all bony fishes (Osteichthyes). The lobe-finned ancestors of the tetrapods evolved them further, while the ancestors of the ray-finned fishes (Actinopterygii) evolved their fins in a different direction. The most primitive group of actinopterygians, the bichirs, still have fleshy frontal fins.

Fossils of early tetrapods

Nine genera of Devonian tetrapods have been described, several known mainly or entirely from lower jaw material. All but one were from the Laurasian supercontinent, which comprised Europe, North America and Greenland. The only exception is a single Gondwanan genus, Metaxygnathus, which has been found in Australia.

The first Devonian tetrapod identified from Asia was recognized from a fossil jawbone reported in 2002. The Chinese tetrapod Sinostega pani was discovered among fossilized tropical plants and lobe-finned fish in the red sandstone sediments of the Ningxia Hui Autonomous Region of northwest China. This finding substantially extended the geographical range of these animals and has raised new questions about the worldwide distribution and great taxonomic diversity they achieved within a relatively short time.

These earliest tetrapods were not terrestrial. The earliest confirmed terrestrial forms are known from the early Carboniferous deposits, some 20 million years later. Still, they may have spent very brief periods out of water and would have used their legs to paw their way through the mud.

Why they went to land in the first place is still debated. One reason could be that the small juveniles who had completed their metamorphosis had what it took to make use of what land had to offer. Already adapted to breathe air and move around in shallow waters near land as a protection (just as modern fish (and amphibians) often spent the first part of their life in the comparative safety of shallow waters like mangrove forests), two very different niches partially overlapped each other, with the young juveniles in the diffuse line between. One of them was overcrowded and dangerous while the other was much safer and much less crowded, offering less competition over resources. The terrestrial niche was also a much more challenging place for primary aquatic animals, but because of the way evolution and the selection pressure works, those juveniles who could take advantage of this would be rewarded. Once they gained a small foothold on land, thanks to their preadaptations and being at the right place at the right time, favourable variations in their descendants would gradually result in continuing evolution and diversification.

At this time the abundance of invertebrates crawling around on land and near water, in moist soil and wet litter, offered a food supply. Some were even big enough to eat small tetrapods, but the land was free from dangers common in the water.

From water to land

Initially making only tentative forays onto land, tetrapods adapted to terrestrial environments over time and spent longer periods away from the water. It is also possible that the adults started to spend some time on land (as the skeletal modifications in early tetrapods such as Ichthyostega suggests) to bask in the sun close to the water's edge, while otherwise being mostly aquatic.

Carboniferous tetrapods

Until the 1990s, there was a 30 million year gap in the fossil record between the late Devonian tetrapods and the reappearance of tetrapod fossils in recognizable mid-Carboniferous amphibian lineages. It was referred to as "Romer's Gap", which now covers the period from about 360 to 345 million years ago (the Devonian-Carboniferous transition and the early Mississippian), after the palaeontologist who recognized it.
During the "gap", tetrapod backbones developed, as did limbs with digits and other adaptations for terrestrial life. Ears, skulls and vertebral columns all underwent changes too. The number of digits on hands and feet became standardized at five, as lineages with more digits died out. The very few tetrapod fossils found in the "gap" are all the more precious.

The transition from an aquatic lobe-finned fish to an air-breathing amphibian was a momentous occasion in the evolutionary history of the vertebrates. For an animal to live in a gravity-neutral, aqueous environment and then invade one that is entirely different required major changes to the overall body plan, both in form and in function. Eryops is an example of an animal that made such adaptations. It retained and refined most of the traits found in its fish ancestors. Sturdy limbs supported and transported its body while out of water. A thicker, stronger backbone prevented its body from sagging under its own weight. Also, by utilizing vestigial fish jaw bones, a rudimentary ear was developed, allowing Eryops to hear airborne sound.

By the Visean age of mid-Carboniferous times the early tetrapods had radiated into at least three main branches. Recognizable basal-group tetrapods are representative of the temnospondyls (e.g. Eryops) lepospondyls (e.g. Diplocaulus) and anthracosaurs, which were the relatives and ancestors of the Amniota. Depending on whichever authorities one follows, modern amphibians (frogs, salamanders and caecilians) are derived from either temnospondyls or lepospondyls (or possibly both, although this is now a minority position).

The first amniotes are known from the early part of the Late Carboniferous, and during the Triassic counted among their number the earliest mammals, turtles, crocodiles (lizards and birds appeared in the Jurassic, and snakes in the Cretaceous), and a fourth Carboniferous group, the baphetids, which are thought related to temnospondyls, left no modern survivors.

Amphibians and reptiles were affected by the Carboniferous Rainforest Collapse (CRC), an extinction event that occurred ~300 million years ago. The sudden collapse of a vital ecosystem shifted the diversity and abundance of major groups. Several large groups, labyrinthodont amphibians were particularly devastated, while the first reptiles fared better, being ecologically adapted to the drier conditions that followed. Amphibians must return to water to lay eggs, in contrast, reptiles - whose amniote eggs have a membrane ensuring gas exchange out of water and can therefore be laid on land - were better adapted to the new conditions. Reptiles invaded new niches at a faster rate and began diversifying their diets, developing herbivory and carnivory, previously only having been insectivores and piscivores.[49]

Permian tetrapods

In the Permian period, in addition to temnospondyl and anthracosaur clades among the early "amphibia" (labyrinthodonts), there were two important clades of amniotes, the Sauropsida and the Synapsida. The latter were the most important and successful Permian animals.
The end of the Permian saw a major turnover in fauna during the Permian–Triassic extinction event. There was a protracted loss of species, due to multiple extinction pulses.[50] Many of the once large and diverse groups died out or were greatly reduced.

Mesozoic tetrapods

Life on Earth seemed to recover quickly after the Permian extinctions, but this was mostly in the form of disaster taxa, such as the hardy Lystrosaurus; specialized animals that formed complex ecosystems, with high biodiversity, complex food webs and a variety of niches, took much longer to recover.[50] Current research indicates that this long recovery was due to successive waves of extinction, which inhibited recovery, and to prolonged environmental stress to organisms that continued into the Early Triassic. Recent research indicates that recovery did not begin until the start of the mid-Triassic, 4M to 6M years after the extinction;[51] and some writers estimate that the recovery was not complete until 30M years after the P-Tr extinction, i.e. in the late Triassic.[50]

A small group of reptiles, the diapsids, began to diversify during the Triassic, notably the dinosaurs. By the late Mesozoic, the large labyrinthodont groups that first appeared during the Paleozoic such as temnospondyls and reptile-like amphibians had gone extinct. All current major groups of sauropsids evolved during the Mesozoic, with birds first appearing in the Jurassic as a derived clade of theropod dinosaurs. Many groups of synapsids such as anomodonts and therocephalians that once comprised the dominant terrestrial fauna of the Permian also became extinct during the Mesozoic; during the Triassic, however, one group (Cynodontia) gave rise to the descendant taxon Mammalia, which survived through the Mesozoic to later diversify during the Cenozoic.

Cenozoic tetrapods

Extant (living) tetrapods

Following the great faunal turnover at the end of the Mesozoic, only six major groups of tetrapods were left, all of which also include many extinct groups:

New evidence emerges on the origins of life

Original link:  http://phys.org/news/2015-06-evidence-emerges-life.html


New evidence emerges on the origins of life



New research shows that the close linkage between the physical properties of amino acids,the genetic code, and protein folding was likely the key factor in the evolution frombuilding blocks to organisms in Earth's primordial soup. Credit: Gerald Prins


In the beginning, there were simple chemicals. And they produced amino acids that eventually became the proteins necessary to create single cells. And the single cells became plants and animals. Recent research is revealing how the primordial soup created the amino acid building blocks, and there is widespread scientific consensus on the evolution from the first cell into plants and animals. But it's still a mystery how the building blocks were first assembled into the proteins that formed the machinery of all cells. Now, two long-time University of North Carolina scientists - Richard Wolfenden, PhD, and Charles Carter, PhD - have shed new light on the transition from building blocks into life some 4 billion years ago.

"Our work shows that the close linkage between the of amino acids, the , and protein folding was likely essential from the beginning, long before large, sophisticated molecules arrived on the scene," said Carter, professor of biochemistry and biophysics at the UNC School of Medicine. "This close interaction was likely the key factor in the evolution from building blocks to organisms."

Their findings, published in companion papers in the Proceedings of the National Academy of Sciences, fly in the face of the problematic "RNA world" theory, which posits that RNA - the molecule that today plays roles in coding, regulating, and expressing genes - elevated itself from the primordial soup of amino acids and cosmic chemicals to give rise first to short proteins called peptides and then to single-celled organisms.

Wolfenden and Carter argue that RNA did not work alone; in fact, it was no more likely that RNA catalyzed peptide formation than it was for peptides to catalyze RNA formation.

The finding adds a new layer to the story of how life evolved billions of years ago.

Its name was LUCA

The scientific community recognizes that 3.6 billion years ago there existed the last universal common ancestor, or LUCA, of all living things presently on Earth. It was likely a single-cell organism. It had a few hundred genes. It already had complete blueprints for DNA replication, protein synthesis, and RNA transcription. It had all the basic components - such as lipids - that modern organisms have. From LUCA forward, it's relatively easy to see how life as we know it evolved.

Before 3.6 billion years, however, there is no hard evidence about how LUCA arose from a boiling caldron of chemicals that formed on Earth after the creation of the planet about 4.6 billion years ago. Those chemicals reacted to form amino acids, which remain the building blocks of proteins in our own cells today.

"We know a lot about LUCA and we are beginning to learn about the chemistry that produced like amino acids, but between the two there is a desert of knowledge," Carter said. "We haven't even known how to explore it."

The UNC research represents an outpost in that desert.

"Dr. Wolfenden established physical properties of the twenty amino acids, and we have found a link between those properties and the genetic code," Carter said. "That link suggests to us that there was a second, earlier code that made possible the peptide-RNA interactions necessary to launch a selection process that we can envision creating the first life on Earth."

Thus, Carter said, RNA did not have to invent itself from the . Instead, even before there were cells, it seems more likely that there were interactions between amino acids and nucleotides that led to the co-creation of proteins and RNA.

Complexity from simplicity

Proteins must fold in specific ways to function properly. The first PNAS paper, led by Wolfenden, shows that both the polarities of the twenty amino acids (how they distribute between water and oil) and their sizes help explain the complex process of protein folding - when a chain of connected amino acids arranges itself to form a particular 3-dimensional structure that has a specific biological function.

"Our experiments show how the polarities of amino acids change consistently across a wide range of temperatures in ways that would not disrupt the basic relationships between genetic coding and ," said Wolfenden, Alumni Distinguished Professor of Biochemistry and Biophysics. This was important to establish because when life was first forming on Earth, temperatures were hot, probably much hotter than they are now or when the first plants and animals were established.

A series of biochemical experiments with amino acids conducted in Wolfenden's lab showed that two properties - the sizes as well as the polarities of amino acids - were necessary and sufficient to explain how the amino acids behaved in folded proteins and that these relationships also held at the higher temperatures of Earth 4 billion years ago.

The second PNAS paper, led by Carter, delves into how enzymes called aminoacyl-tRNA synthetases recognized transfer ribonucleic acid, or tRNA. Those enzymes translate the genetic code.

"Think of tRNA as an adapter," Carter said. "One end of the adapter carries a particular amino acid; the other end reads the genetic blueprint for that amino acid in messenger RNA. Each synthetase matches one of the twenty amino acids with its own adapter so that the genetic blueprint in messenger RNA faithfully makes the correct every time."

Carter's analysis shows that the two different ends of the L-shaped tRNA molecule contained independent codes or rules that specify which amino acid to select. The end of tRNA that carried the amino acid sorted amino acids specifically according to size.

The other end of the L-shaped tRNA molecule is called the tRNA anticodon. It reads codons, which are sequences of three RNA nucleotides in genetic messages that select amino acids according to polarity.

Wolfenden and Carter's findings imply that the relationships between tRNA and the physical properties of the - their sizes and polarities - were crucial during the Earth's primordial era. In light of Carter's previous work with very small active cores of tRNA synthetases called Urzymes, it now seems likely that selection by size preceded selection according to polarity. This ordered selection meant that the earliest proteins did not necessarily fold into unique shapes, and that their unique structures evolved later.

Carter said, "Translating the genetic code is the nexus connecting pre-biotic chemistry to biology."

He and Wolfenden believe that the intermediate stage of genetic coding can help resolve two paradoxes: how complexity arose from simplicity, and how life divided the labor between two very different kinds of polymers: proteins and nucleic acids.

"The fact that genetic coding developed in two successive stages - the first of which was relatively simple - may be one reason why life was able to emerge while the earth was still quite young," Wolfenden noted.

An earlier code, which enabled the earliest coded peptides to bind RNA, may have furnished a decisive selective advantage. And this primitive system could then undergo a natural selection process, thereby launching a new and more biological form of evolution.

"The collaboration between RNA and peptides was likely necessary for the spontaneous emergence of complexity," Carter added. "In our view, it was a peptide-RNA world, not an RNA-only world."


More information: Temperature dependence of amino acid hydrophobicities, www.pnas.org/cgi/doi/10.1073/pnas.1507565112

tRNA acceptor stem and anticodon bases form independent codes related to protein folding, www.pnas.org/cgi/doi/10.1073/pnas.1507569112

Sunday, May 31, 2015

Marine biology


From Wikipedia, the free encyclopedia

Two views of the ocean from space
Only 29 percent of the Earth's surface is land. The rest is ocean, home to marine life. The oceans average nearly four kilometres in depth and are fringed with coastlines that run for 360,000 kilometres.[1][2]

Marine biology is the scientific study of organisms in the ocean or other marine or brackish bodies of water. Given that in biology many phyla, families and genera have some species that live in the sea and others that live on land, marine biology classifies species based on the environment rather than on taxonomy. Marine biology differs from marine ecology as marine ecology is focused on how organisms interact with each other and the environment, while biology is the study of the organisms themselves.

A large proportion of all life on Earth exists in the ocean. Exactly how large the proportion is unknown, since many ocean species are still to be discovered. The ocean is a complex three-dimensional world[3] covering about 71% of the Earth's surface. The habitats studied in marine biology include everything from the tiny layers of surface water in which organisms and abiotic items may be trapped in surface tension between the ocean and atmosphere, to the depths of the oceanic trenches, sometimes 10,000 meters or more beneath the surface of the ocean. Specific habitats include coral reefs, kelp forests, seagrass meadows, the surrounds of seamounts and thermal vents, tidepools, muddy, sandy and rocky bottoms, and the open ocean (pelagic) zone, where solid objects are rare and the surface of the water is the only visible boundary. The organisms studied range from microscopic phytoplankton and zooplankton to huge cetaceans (whales) 30 meters (98 feet) in length.

Marine life is a vast resource, providing food, medicine, and raw materials, in addition to helping to support recreation and tourism all over the world. At a fundamental level, marine life helps determine the very nature of our planet. Marine organisms contribute significantly to the oxygen cycle, and are involved in the regulation of the Earth's climate.[4] Shorelines are in part shaped and protected by marine life, and some marine organisms even help create new land.[5]

Many species are economically important to humans, including food fish (both finfish and shellfish). It is also becoming understood that the well-being of marine organisms and other organisms are linked in very fundamental ways. The human body of knowledge regarding the relationship between life in the sea and important cycles is rapidly growing, with new discoveries being made nearly every day. These cycles include those of matter (such as the carbon cycle) and of air (such as Earth's respiration, and movement of energy through ecosystems including the ocean). Large areas beneath the ocean surface still remain effectively unexplored.

History


HMS Challenger during its pioneer expedition of 1872–76

Early instances of the study of marine biology trace back to Aristotle (384–322 BC) who made several contributions which laid the foundation for many future discoveries and were the first big step in the early exploration period of the ocean and marine life.[6] In 1768, Samuel Gottlieb Gmelin (1744–1774) published the Historia Fucorum, the first work dedicated to marine algae and the first book on marine biology to use the then new binomial nomenclature of Linnaeus. It included elaborate illustrations of seaweed and marine algae on folded leaves.[7][8] The British naturalist Edward Forbes (1815–1854) is generally regarded as the founder of the science of marine biology.[9] The pace of oceanographic and marine biology studies quickly accelerated during the course of the 19th century.

The observations made in the first studies of marine biology fuelled the age of discovery and exploration that followed. During this time, a vast amount of knowledge was gained about the life that exists in the oceans of the world. Many voyages contributed significantly to this pool of knowledge. Among the most significant were the voyages of the HMS Beagle where Charles Darwin came up with his theories of evolution and on the formation of coral reefs.[10] Another important expedition was undertaken by HMS Challenger, where findings were made of unexpectedly high species diversity among fauna stimulating much theorizing by population ecologists on how such varieties of life could be maintained in what was thought to be such a hostile environment.[11] This era was important for the history of marine biology but naturalists were still limited in their studies because they lacked technology that would allow them to adequately examine species that lived in deep parts of the oceans.

The creation of marine laboratories was important because it allowed marine biologists to conduct research and process their specimens from expeditions. The oldest marine laboratory in the world, Station biologique de Roscoff, was established in France in 1872. In the United States, the Scripps Institution of Oceanography dates back to 1903, while the prominent Woods Hole Oceanographic Institute was founded in 1930.[12] The development of technology such as sound navigation ranging, scuba diving gear, submersibles and remotely operated vehicles allowed marine biologists to discover and explore life in deep oceans that was once thought to not exist.[13]

Subfields


Coral reefs form complex marine ecosystems with tremendous biodiversity.

The marine ecosystem is large, and thus there are many sub-fields of marine biology. Most involve studying specializations of particular animal groups, such as phycology, invertebrate zoology and ichthyology.

Other subfields study the physical effects of continual immersion in sea water and the ocean in general, adaptation to a salty environment, and the effects of changing various oceanic properties on marine life. A subfield of marine biology studies the relationships between oceans and ocean life, and global warming and environmental issues (such as carbon dioxide displacement).

Recent marine biotechnology has focused largely on marine biomolecules, especially proteins, that may have uses in medicine or engineering. Marine environments are the home to many exotic biological materials that may inspire biomimetic materials.

Related fields

Marine biology is a branch of biology and is closely linked to oceanography. It also encompasses many ideas from ecology. Fisheries science and marine conservation can be considered partial offshoots of marine biology (as well as environmental studies). Marine Chemistry, Physical oceanography and Atmospheric sciences are closely related to this field.

Animals

Birds

Birds adapted to living in the marine environment are often called seabirds. Examples include albatross, penguins, gannets, and auks. Although they spend most of their lives in the ocean, species such as gulls can often be found thousands of miles inland.

Fish

Fish anatomy includes a two-chambered heart, operculum, swim bladder, scales, fins, lips, eyes and secretory cells that produce mucous. Fish breathe by extracting oxygen from water through their gills. Fins propel and stabilize the fish in the water. Many fish fall under two major categories - Elasmobranchii and Teleostei.
A reported 32,700 species of fish have been described (as of December 2013),[14] more than the combined total of all other vertebrates. About 60% of fish species are saltwater fish.[15]

Invertebrates

As on land, invertebrates make up a huge portion of all life in the sea. Invertebrate sea life includes Cnidaria such as jellyfish and sea anemones; Ctenophora; sea worms including the phyla Platyhelminthes, Nemertea, Annelida, Sipuncula, Echiura, Chaetognatha, and Phoronida; Mollusca including shellfish, squid, octopus; Arthropoda including Chelicerata and Crustacea; Porifera; Bryozoa; Echinodermata including starfish; and Urochordata including sea squirts or tunicates.

Mammals

There are five main types of marine mammals.

Reptiles

Reptiles which inhabit or frequent the sea include sea turtles, sea snakes, terrapins, the marine iguana, and the saltwater crocodile. Most extant marine reptiles, except for some sea snakes, are oviparous and need to return to land to lay their eggs. Thus most species, excepting sea turtles, spend most of their lives on or near land rather than in the ocean. Despite their marine adaptations, most sea snakes prefer shallow waters nearby land, around islands, especially waters that are somewhat sheltered, as well as near estuaries.[16][17] Some extinct marine reptiles, such as ichthyosaurs, evolved to be viviparous and had no requirement to return to land.

Fungi

Over 1500 species of fungi are known from marine environments.[18] These parasitize marine algae or animals, or are saprobes on algae, corals, protozoan cysts, sea grasses, wood and other substrata, and can also be found in sea foam.[19] Spores of many species have special appendages which facilitate attachment to the substratum.[20] A very diverse range of unusual secondary metabolites is produced by marine fungi.[21]

Plants and algae

Microscopic algae and plants provide important habitats for life, sometimes acting as hiding and foraging places for larval forms of larger fish and invertebrates.

Algal life is widespread and very diverse under the ocean. Microscopic photosynthetic algae contribute a larger proportion of the world's photosynthetic output than all the terrestrial forests combined. Most of the niche occupied by sub plants on land is actually occupied by macroscopic algae in the ocean, such as Sargassum and kelp, which are commonly known as seaweeds that creates kelp forests.

Plants that survive in the sea are often found in shallow waters, such as the seagrasses (examples of which are eelgrass, Zostera, and turtle grass, Thalassia). These plants have adapted to the high salinity of the ocean environment. The intertidal zone is also a good place to find plant life in the sea, where mangroves or cordgrass or beach grass might grow. Microscopic algae and plants provide important habitats for life, sometimes acting as hiding and foraging places for larval forms of larger fish and invertebrates.

Microscopic life



Microscopic life undersea is incredibly diverse and still poorly understood. For example, the role of viruses in marine ecosystems is barely being explored even in the beginning of the 21st century.[22]

The role of phytoplankton is better understood due to their critical position as the most numerous primary producers on Earth. Phytoplankton are categorized into cyanobacteria (also called blue-green algae/bacteria), various types of algae (red, green, brown, and yellow-green), diatoms, dinoflagellates, euglenoids, coccolithophorids, cryptomonads, chrysophytes, chlorophytes, prasinophytes, and silicoflagellates.

Zooplankton tend to be somewhat larger, and not all are microscopic. Many Protozoa are zooplankton, including dinoflagellates, zooflagellates, foraminiferans, and radiolarians. Some of these (such as dinoflagellates) are also phytoplankton; the distinction between plants and animals often breaks down in very small organisms. Other zooplankton include cnidarians, ctenophores, chaetognaths, molluscs, arthropods, urochordates, and annelids such as polychaetes. Many larger animals begin their life as zooplankton before they become large enough to take their familiar forms. Two examples are fish larvae and sea stars (also called starfish).

Marine habitats

Marine habitats can be divided into coastal and open ocean habitats. Coastal habitats are found in the area that extends from the shoreline to the edge of the continental shelf. Most marine life is found in coastal habitats, even though the shelf area occupies only seven percent of the total ocean area. Open ocean habitats are found in the deep ocean beyond the edge of the continental shelf. Alternatively, marine habitats can be divided into pelagic and demersal habitats. Pelagic habitats are found near the surface or in the open water column, away from the bottom of the ocean. Demersal habitats are near or on the bottom of the ocean. An organism living in a pelagic habitat is said to be a pelagic organism, as in pelagic fish. Similarly, an organism living in a demersal habitat is said to be a demersal organism, as in demersal fish. Pelagic habitats are intrinsically shifting and ephemeral, depending on what ocean currents are doing.

Marine habitats can be modified by their inhabitants. Some marine organisms, like corals, kelp and seagrasses, are ecosystem engineers which reshape the marine environment to the point where they create further habitat for other organisms.

Intertidal and shore


Tide pools with sea stars and sea anemone in Santa Cruz, California

Intertidal zones, those areas close to shore, are constantly being exposed and covered by the ocean's tides. A huge array of life lives within this zone.

Shore habitats span from the upper intertidal zones to the area where land vegetation takes prominence. It can be underwater anywhere from daily to very infrequently. Many species here are scavengers, living off of sea life that is washed up on the shore. Many land animals also make much use of the shore and intertidal habitats. A subgroup of organisms in this habitat bores and grinds exposed rock through the process of bioerosion.

Reefs

Reefs comprise some of the densest and most diverse habitats in the world. The best-known types of reefs are tropical coral reefs which exist in most tropical waters; however, reefs can also exist in cold water. Reefs are built up by corals and other calcium-depositing animals, usually on top of a rocky outcrop on the ocean floor. Reefs can also grow on other surfaces, which has made it possible to create artificial reefs. Coral reefs also support a huge community of life, including the corals themselves, their symbiotic zooxanthellae, tropical fish and many other organisms.
Much attention in marine biology is focused on coral reefs and the El Niño weather phenomenon. In 1998, coral reefs experienced the most severe mass bleaching events on record, when vast expanses of reefs across the world died because sea surface temperatures rose well above normal.[23][24] Some reefs are recovering, but scientists say that between 50% and 70% of the world's coral reefs are now endangered and predict that global warming could exacerbate this trend.[25][26][27][28]

Open ocean

The open ocean is relatively unproductive because of a lack of nutrients, yet because it is so vast, in total it produces the most primary productivity. Much of the aphotic zone's energy is supplied by the open ocean in the form of detritus.

Deep sea and trenches

The deepest recorded oceanic trench measured to date is the Mariana Trench, near the Philippines, in the Pacific Ocean at 10,924 m (35,840 ft). At such depths, water pressure is extreme and there is no sunlight, but some life still exists. A white flatfish, a shrimp and a jellyfish were seen by the American crew of the bathyscaphe Trieste when it dove to the bottom in 1960.[29]

Other notable oceanic trenches include Monterey Canyon, in the eastern Pacific, the Tonga Trench in the southwest at 10,882 m (35,702 ft), the Philippine Trench, the Puerto Rico Trench at 8,605 m (28,232 ft), the Romanche Trench at 7,760 m (25,460 ft), Fram Basin in the Arctic Ocean at 4,665 m (15,305 ft), the Java Trench at 7,450 m (24,440 ft), and the South Sandwich Trench at 7,235 m (23,737 ft).

In general, the deep sea is considered to start at the aphotic zone, the point where sunlight loses its power of transference through the water.[citation needed] Many life forms that live at these depths have the ability to create their own light known as bio-luminescence.

Marine life also flourishes around seamounts that rise from the depths, where fish and other sea life congregate to spawn and feed. Hydrothermal vents along the mid-ocean ridge spreading centers act as oases, as do their opposites, cold seeps. Such places support unique biomes and many new microbes and other lifeforms have been discovered at these locations .[citation needed]

Distribution factors

An active research topic in marine biology is to discover and map the life cycles of various species and where they spend their time. Technologies that aid in this discovery include pop-up satellite archival tags, acoustic tags, and a variety of other data loggers. Marine biologists study how the ocean currents, tides and many other oceanic factors affect ocean life forms, including their growth, distribution and well-being. This has only recently become technically feasible with advances in GPS and newer underwater visual devices.[citation needed]

Most ocean life breeds in specific places, nests or not in others, spends time as juveniles in still others, and in maturity in yet others. Scientists know little about where many species spend different parts of their life cycles especially in the infant and juvenile years. For example, it is still largely unknown where juvenile sea turtles and some year-1 sharks travel. Recent advances in underwater tracking devices are illuminating what we know about marine organisms that live at great Ocean depths.[30] The information that pop-up satellite archival tags give aids in certain time of the year fishing closures and development of a marine protected area. This data is important to both scientists and fishermen because they are discovering that by restricting commercial fishing in one small area they can have a large impact in maintaining a healthy fish population in a much larger area.