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Loganair

Loganair is a Scottish regional airline headquartered at Glasgow Airport in Paisley, Scotland. The airline primarily operates domestic flights within the United Kingdom. It is the largest regional airline in the United Kingdom by passenger numbers and fleet size.

In addition to its main base at Glasgow, it has hubs at Aberdeen, Edinburgh, Inverness and Newcastle airports. It holds a United Kingdom Civil Aviation Authority Type A Operating Licence, permitting it to carry passengers, cargo and mail on aircraft with 20 or more seats.

Early years
Loganair was established on 1 February 1962 by Willie Logan of the Logan Construction Company Ltd, operating as its air charter arm with a Piper PA-23 Aztec based at Edinburgh.

In 1967, Loganair took delivery of three Britten-Norman Islander twin-engine eight-seat light commuter airliners and began regular flights between the Orkney Islands, and started operating in Shetland in 1970. In 1966, after Renfrew Airport closed, the airline established its head office at Glasgow Airport. This aspect of Loganair's operations ceased on 31 March 2006 when the new contract for air ambulance work was awarded to Gama Aviation.

Between 1968 and 1983, the company was owned by the Royal Bank of Scotland, Towards the end of this period, Loganair bought Short 360 and Fokker F27 Friendship aircraft. The company brought jet aircraft into the fleet with two British Aerospace 146s. In December 1983 it became a subsidiary of the Airlines of Britain Group. Further aircraft were added to the fleet: British Aerospace Jetstream 31, British Aerospace Jetstream 41, and British Aerospace ATP aircraft. In the late 1980s Loganair was the fastest-growing scheduled operator at Manchester Airport, and, in terms of number of flights, was the airport's second-busiest carrier.

In 1993, the airline became a franchisee of British Airways, operating its Islanders in the British Airways livery. This would stand until July 2008, when it became the new franchisee of Flybe.

After a restructure of British Midland Group in 1994, Loganair's routes outside Scotland and the aircraft used to operate them were transferred to Manx Airlines. This consolidation of services led to the formation of a new airline, British Regional Airline (BRA Ltd). In 1997, with Loganair now consisting of six aircraft (one de Havilland Canada DHC-6 Twin Otter and five Britten Norman Islanders) and 44 staff, a management buy-out occurred.

Operations as Flybe franchise
In June 2005, Loganair was awarded a contract from the Irish Government to operate a daily return service from Knock, County Mayo to Dublin. This public service obligation (PSO) route operated for a period of three years as British Airways, with effect from 22 July 2005. The operation ceased in July 2008, the contract having been lost to Aer Arann. The airline also bought routes from Citiexpress in March 2004.

Until October 2008, Loganair was a British Airways franchisee, operating flights sold through BA using BA flight codes. Loganair's inter-island operations between the Orkney and Shetland Islands carried out using Britten-Norman Islanders were removed from the franchise agreement in 2004. The flights have since been marketed under Loganair's own name, rather than British Airways'. Loganair became a franchise airline of Flybe, operating in the Flybe colours. Flights are also operated under a codeshare agreement with British Airways connecting flights from Scotland to London. The franchise has been criticised by residents in the Scottish islands for what they perceive to be excessively high fares, and a Facebook campaign set up in June 2015 to highlight the issue attracted over 7400 "likes" over the course of its first weekend.

Purchase of ScotAirways
On 8 July 2011, it was announced that Loganair had agreed to purchase Cambridge based ScotAirways. ScotAirways continued to trade as a separate entity (using its original name of Suckling Airways) and holding its own licences and approvals until April 2013.

Services to Belfast and to Birmingham from Dundee ended on 2 December 2012. After CityJet had terminated its services between Dundee and London City Airport in January 2014, Loganair took over the route, operating from Dundee to London Stansted Airport, with the support of a PSO agreement.

In May 2015, two Viking Air DHC-6-400 Twin Otter aircraft were acquired by Highlands and Islands Airports to be operated by Loganair on the Scottish Government's Public Service Obligation routes between Glasgow and Campbeltown, Tiree and Barra. In August 2015 the airline became part of a new regional airline group, Airline Investments Limited (AIL), along with East Midlands-based airline bmi regional.

On 21 November 2016, Flybe and Loganair announced that their franchise agreement would terminate on 31 August 2017. Despite headlines, it is unclear who initiated the termination. Loganair later relaunched its website without renewed interline agreements with Flybe or Aer Lingus.

In April 2017, pending the termination of the Flybe franchise agreement, Loganair unveiled its new independent corporate livery on Saab 340B Freighter G-LGNN. From 1 September the airline began operating "in its own right" for the first time in 24 years. Loganair signed a codeshare agreement with British Airways (BA), effective from 1 September 2017 (coinciding with the launch of independent operations), allowing passengers to book through flights onto BA's global network.

Reactions to the demise of other airlines
In February 2019, following Flybmi's cessation of operations, Loganair announced that it was to take over Flybmi's routes from Aberdeen to Bristol, Oslo and Esbjerg, from Newcastle to Stavanger and Brussels, and from City of Derry Airport to London-Stansted. A BALPA tribunal into Loganair's swift action following the closure of Flybmi found that the carrier had been acting lawfully, despite the fact that it had created several contingency plans for the demise of UK airlines Eastern Airways and Flybe.

In March 2020, following Flybe's cessation of operations, Loganair announced that it was to take over several Flybe routes from Scotland and Newcastle.

Potential sale
In October 2022, Loganair confirmed that the existing sole owners, brothers Stephen (age 72) and Peter Bond (age 61), were seeking a buyer to act as the company's "custodian for the next generation". The sale process was suspended in October 2023, with the Bond brothers retaining their stake while a fleet renewal programme is completed.

Destinations
, Loganair serves 44 destinations in the United Kingdom, the Isle of Man, the Republic of Ireland and continental Europe. Part of Loganair's operations includes the world's shortest scheduled commercial route, between Westray Airport and Papa Westray Airport, a distance of 1.7 miles, and the use of Barra Airport, the only airport in the world to use a beach as a runway. After the collapse of the original Flybe in March 2020, Loganair took over a number of former Flybe routes from Scotland, the North of England and other parts of the UK, with service beginning as little as 10 days later.

In March 2023, Loganair secured a lease from British Airways for 30 additional slot pairs at Heathrow, previously leased to the relaunched Flybe before its demise in January 2023, and called on the UK government to reform competition remedies in order to ensure that Heathrow slots remain permanently available for UK regional connectivity.

Codeshare agreements
Loganair has codeshare agreements with the following airlines (as of April 2022):

 * Aurigny
 * Blue Islands
 * British Airways
 * KLM

Interline agreements
Loganair has interline agreements with the following airlines (as of November 2023):

 * Aer Lingus
 * Air France
 * Air Transat
 * Emirates
 * Etihad Airways
 * Ethiopian Airlines
 * Finnair
 * Hainan Airlines
 * Icelandair
 * Luxair
 * Qatar Airways
 * Singapore Airlines
 * Turkish Airlines
 * United Airlines
 * Widerøe

Current fleet
, the Loganair fleet consists of the following aircraft:

Fleet development
In June 2018, Loganair announced plans to add two additional Embraer ERJ-145 aircraft for summer 2019. The aircraft were to be transferred from sister company Flybmi, and would initially operate flights from Loganair's Glasgow base to Derry and Stornoway. Loganair also planned to use the Embraer ERJ-145 aircraft to launch new routes to European airports not previously served from Glasgow. In November 2018, the company announced that approximately twenty ATR 42 aircraft would be added to replace the Saab 2000 and Saab 340 aircraft in the third quarter of 2019.

In April 2019, its Dornier 328 fleet was withdrawn and stored. Loganair returned the last of its Saab 2000 aircraft to the lessor on 25 March 2020.

Its Saab 340s were retired in January 2024, to be replaced by 8 new ATRs which will complement the existing ATR fleet. In January 2024, Loganair announced plans to introduce a hydrogen fuel cell-powered Britten-Norman BN-2 Islander on its Orkney island-hopping routes by 2027. The aircraft could be either a new build or a conversion of one of the airline's existing Islanders.

Accidents and incidents

 * On 12 June 1986, a DHC-6 Twin Otter aircraft with 16 people on board struck high ground on the island of Islay in poor weather. The pilots had mistakenly identified the coastal village of Laphroaig as the town of Port Ellen, near Islay's Glenegedale Airport. There was one fatality, a pilot.
 * In 1996, a Britten-Norman Islander was destroyed in Shetland. The accident occurred during a night time return flight to the aircraft's home base following a medical evacuation flight. The aircraft crashed short of the runway whilst attempting to land after a previous discontinued approach in strong gusting cross winds. The pilot had exercised his discretion to extend the period for which he was allowed to fly that day. The pilot's medical certificate had expired nineteen days earlier thus invalidating his pilot's licence. The pilot was killed in the crash and a doctor on board was seriously injured; a nurse seated at the rear of the aircraft sustained minor injuries.
 * On 27 February 2001, Flight 670, a Short 360 registered G-BNMT operating a Royal Mail flight to Belfast, crashed into the Firth of Forth shortly after taking off from Edinburgh at 1730GMT. Both crew members were killed. There were no passengers on board. An Air Accidents Investigation Branch (AAIB) inquiry later blamed a buildup of slush in the aircraft's engines for the crash. Protective covers had not been fitted to the engine intakes while the aircraft was parked for several hours in heavy snow at Edinburgh.
 * On 15 March 2005, a Britten-Norman Islander crashed into the sea while descending toward Campbeltown Airport in western Scotland. The aircraft was operating on an unscheduled air ambulance flight. Both occupants, the pilot and one passenger (a paramedic with the Scottish Ambulance Service), died in the crash. As a result of this accident, the European Aviation Safety Agency (EASA) accepted Safety Recommendation UNKG-2006-101 from the UK's accident investigation report, which the European Commission adopted into regulation, making passenger shoulder harnesses mandatory on all commercial air transport aircraft weighing less than 5700 kg and having fewer than nine passenger seats.
 * On 15 December 2014, Flight 6780, a Saab 2000 registered G-LGNO, was struck by lightning whilst approaching Sumburgh Airport. The flight subsequently suffered from control difficulties and nosedived from 4000 to 1000 ft after the crew tried taking over the controls, but failed to achieve control. The pilot was under the belief that a lightning strike would automatically disengage the autopilot, and the control difficulties were due to opposition from the autopilot system trying to bring them back to the preprogrammed altitude, and it was determined that they only regained control due to a computer malfunction disabling the autopilot system. Once control was regained, they were able to safely return to Aberdeen. There were 33 occupants onboard and no injuries were reported. The subsequent investigation into the incident also revealed that the Saab 2000 was the only Saab model at the time that did not automatically disengage the autopilot with pilot manual control input.
 * On 16 June 2020, a Loganair Embraer ERJ-145EP registered as G-SAJS sustained minor damage at its stand on the apron at Aberdeen Airport after it was struck in a low-speed collision by a Bombardier Dash 8 Q400 registered as G-JECK. The Dash 8, wearing the livery of the defunct airline Flybe, became wedged underneath the ERJ's right hand engine. No passengers were aboard either aircraft the time of the collision, and no injuries were reported.

title: Loganair


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Archosaur

Archosauria (lit. 'ruling reptiles') or archosaurs is a clade of diapsid sauropsid tetrapods, with birds and crocodilians being the only extant representatives. Although broadly classified as reptiles, which traditionally exclude birds, the cladistic sense of the term includes all living and extinct relatives of birds and crocodilians such as non-avian dinosaurs, pterosaurs, phytosaurs, aetosaurs and rauisuchians as well as many Mesozoic marine reptiles. Modern paleontologists define Archosauria as a crown group that includes the most recent common ancestor of living birds and crocodilians, and all of its descendants.

The base of Archosauria splits into two clades: Pseudosuchia, which includes crocodilians and their extinct relatives; and Avemetatarsalia, which includes birds and their extinct relatives (such as non-avian dinosaurs and pterosaurs). Older definitions of the group Archosauria rely on shared morphological characteristics, such as an antorbital fenestra in the skull, serrated teeth, and an upright stance. Some extinct reptiles, such as proterosuchids and euparkeriids, also possessed these features yet originated prior to the split between the crocodilian and bird lineages. The older morphological definition of Archosauria nowadays roughly corresponds to Archosauriformes, a group named to encompass crown-group archosaurs and their close relatives.

The oldest true archosaur fossils are known from the Early Triassic period, though the first archosauriforms and archosauromorphs (reptilians closer to archosaurs than to lizards or other lepidosaurs) appeared in the Permian. Archosaurs quickly diversified in the aftermath of the Permian-Triassic mass extinction (~252 Ma), which wiped out most of the then-dominant therapsid competitors such as the gorgonopsians and anomodonts, and the subsequent arid Triassic climate allowed the more drought-resiliant archosaurs (largely due to their uric acid-based urinary system) to eventually become the largest and most ecologically dominant terrestrial vertebrates from the Middle Triassic period up until the Cretaceous–Paleogene extinction event (~66 Ma). Birds and several crocodyliform lineages were the only archosaurs to survive the K-Pg extinction, rediversifying in the subsequent Cenozoic era. Birds in particular have become among the most species-rich groups of terrestrial vertebrates in the present day.

Distinguishing characteristics
Archosaurs can traditionally be distinguished from other tetrapods on the basis of several synapomorphies, or shared characteristics, which were present in their last common ancestor. Many of these characteristics appeared prior to the origin of the clade Archosauria, as they were present in archosauriforms such as Proterosuchus and Euparkeria, which were outside the crown group.

The most obvious features include teeth set in deep sockets, antorbital and mandibular fenestrae (openings in front of the eyes and in the jaw, respectively), and a pronounced fourth trochanter (a prominent ridge on the femur). Being set in sockets, the teeth were less likely to be torn loose during feeding. This feature is responsible for the name "thecodont" (meaning "socket teeth"), which early paleontologists applied to many Triassic archosaurs. Additionally, non-muscular cheek and lip tissue appear in various forms throughout the clade, with all living archosaurs lacking non-muscular lips, unlike most non-avian saurischian dinosaurs. Some archosaurs, such as birds, are secondarily toothless. Antorbital fenestrae reduced the weight of the skull, which was relatively large in early archosaurs, rather like that of modern crocodilians. Mandibular fenestrae may also have reduced the weight of the jaw in some forms. The fourth trochanter provides a large site for the attachment of muscles on the femur. Stronger muscles allowed for erect gaits in early archosaurs, and may also be connected with the ability of the archosaurs or their immediate ancestors to survive the catastrophic Permian-Triassic extinction event.

Unlike their close living relatives, the lepidosaurs, archosaurs lost the vomeronasal organ.

Origins
Archosaurs are a subgroup of archosauriforms, which themselves are a subgroup of archosauromorphs. Both the oldest archosauromorph (Protorosaurus speneri) and the oldest archosauriform (Archosaurus rossicus) lived in the late Permian. The oldest true archosaurs appeared during the Olenekian stage (247–251 Ma) of the Early Triassic. A few fragmentary fossils of large carnivorous crocodilian-line archosaurs (informally termed "rauisuchians") are known from this stage. These include Scythosuchus and Tsylmosuchus (both of which have been found in Russia), as well as the Xilousuchus, a ctenosauriscid from China. The oldest known fossils of bird-line archosaurs are from the Anisian stage (247–242 Ma) of Tanzania, and include Asilisaurus (an early silesaurid), Teleocrater (an aphanosaur), and Nyasasaurus (a possible early dinosaur).

Archosaurian domination in the Triassic
Synapsids are a clade that includes mammals and their extinct ancestors. The latter group are often referred to as mammal-like reptiles, but should be termed protomammals, stem mammals, or basal synapsids, because they are not true reptiles by modern cladistic classification. They were the dominant land vertebrates throughout the Permian, but most perished in the Permian–Triassic extinction event. Very few large synapsids survived the event, but one form, Lystrosaurus (a herbivorous dicynodont), attained a widespread distribution soon after the extinction. Following this, archosaurs and other archosauriforms quickly became the dominant land vertebrates in the early Triassic. Fossils from before the mass extinction have only been found around the Equator, but after the event fossils can be found all over the world. Suggested explanations for this include:
 * Archosaurs made more rapid progress towards erect limbs than synapsids, and this gave them greater stamina by avoiding Carrier's constraint. An objection to this explanation is that archosaurs became dominant while they still had sprawling or semi-erect limbs, similar to those of Lystrosaurus and other synapsids.
 * Archosaurs have more efficient respiratory systems featuring unidirectional air flow, as opposed to the tidal respiration of synapids. The ability to breathe more efficiently in hypoxic conditions may have been advantageous to early archosaurs during the suspected drop in oxygen levels at the end of the Permian.
 * The Early Triassic was predominantly arid, because most of the Earth's land was concentrated in the supercontinent Pangaea. Archosaurs were probably better at conserving water than early synapsids because:
 * Modern diapsids (lizards, snakes, crocodilians, birds) excrete uric acid, which can be excreted as a paste, resulting in low water loss as opposed to a more dilute urine. It is reasonable to suppose that archosaurs (the ancestors of crocodilians, dinosaurs and pterosaurs) also excreted uric acid, and therefore were good at conserving water. The aglandular (glandless) skins of diapsids would also have helped to conserve water.
 * Modern mammals excrete urea, which requires a relatively high urinary rate to keep it from leaving the urine by diffusion in the kidney tubules. Their skins also contain many glands, which also lose water. Assuming that early synapsids had similar features, e.g., as argued by the authors of Palaeos, they were at a disadvantage in a mainly arid world. The same well-respected site points out that "for much of Australia's Plio-Pleistocene history, where conditions were probably similar, the largest terrestrial predators were not mammals but gigantic varanid lizards (Megalania) and land crocs."

However, this theory has been questioned, since it implies synapsids were necessarily less advantaged in water retention, that synapsid decline coincides with climate changes or archosaur diversity (neither of which tested) and the fact that desert dwelling mammals are as well adapted in this department as archosaurs, and some cynodonts like Trucidocynodon were large sized predators. A study favors competition amidst mammaliaforms as the main explanation for Mesozoic mammals being small.

Main forms

Since the 1970s, scientists have classified archosaurs mainly on the basis of their ankles. The earliest archosaurs had "primitive mesotarsal" ankles: the astragalus and calcaneum were fixed to the tibia and fibula by sutures and the joint bent about the contact between these bones and the foot.

The Pseudosuchia appeared early in the Triassic. In their ankles, the astragalus was joined to the tibia by a suture and the joint rotated round a peg on the astragalus which fitted into a socket in the calcaneum. Early "crurotarsans" still walked with sprawling limbs, but some later crurotarsans developed fully erect limbs. Modern crocodilians are crurotarsans that can employ a diverse range of gaits depending on speed.

Euparkeria and the Ornithosuchidae had "reversed crurotarsal" ankles, with a peg on the calcaneum and socket on the astragalus.

The earliest fossils of Avemetatarsalia ("bird ankles") appear in the Anisian age of the Middle Triassic. Most Ornithodirans had "advanced mesotarsal" ankles. This form of ankle incorporated a very large astragalus and very small calcaneum, and could only move in one plane, like a simple hinge. This arrangement, which was only suitable for animals with erect limbs, provided more stability when the animals were running. The earliest avemetatarsalians, such as Teleocrater and Asilisaurus, retained "primitive mesotarsal" ankles. The ornithodirans differed from other archosaurs in other ways: they were lightly built and usually small, their necks were long and had an S-shaped curve, their skulls were much more lightly built, and many ornithodirans were completely bipedal. The archosaurian fourth trochanter on the femur may have made it easier for ornithodirans to become bipeds, because it provided more leverage for the thigh muscles. In the late Triassic, the ornithodirans diversified to produce dinosaurs and pterosaurs.

Modern classification
Archosauria is normally defined as a crown group, which means that it only includes descendants of the last common ancestors of its living representatives. In the case of archosaurs, these are birds and crocodilians. Archosauria is within the larger clade Archosauriformes, which includes some close relatives of archosaurs, such as proterochampsids and euparkeriids. These relatives are often referred to as archosaurs despite being placed outside of the crown group Archosauria in a more basal position within Archosauriformes. Historically, many archosauriforms were described as archosaurs, including proterosuchids and erythrosuchids, based on the presence of an antorbital fenestra. While many researchers prefer to treat Archosauria as an unranked clade, some continue to assign it a traditional biological rank. Traditionally, Archosauria has been treated as a Superorder, though a few 21st century researchers have assigned it to different ranks including Division and Class.

History of classification
Archosauria as a term was first coined by American paleontologist Edward Drinker Cope in 1869, and included a wide range of taxa including dinosaurs, crocodilians, thecodonts, sauropterygians (which may be related to turtles), rhynchocephalians (a group that according to Cope included rhynchosaurs, which nowadays are considered to be more basal archosauromorphs, and tuataras, which are lepidosaurs), and anomodonts, which are now considered synapsids. It was not until 1986 that Archosauria was defined as a crown-clade, restricting its use to more derived taxa.

Cope's term was a Greek-Latin hybrid intended to refer to the cranial arches, but has later also been understood as "leading reptiles" or "ruling reptiles" by association with Greek ἀρχός "leader, ruler".

The term "thecodont", now considered an obsolete term, was first used by the English paleontologist Richard Owen in 1859 to describe Triassic archosaurs, and it became widely used in the 20th century. Thecodonts were considered the "basal stock" from which the more advanced archosaurs descended. They did not possess features seen in later avian and crocodilian lines, and therefore were considered more primitive and ancestral to the two groups. With the cladistic revolution of the 1980s and 90s, in which cladistics became the most widely used method of classifying organisms, thecodonts were no longer considered a valid grouping. Because they are considered a "basal stock", thecodonts are paraphyletic, meaning that they form a group that does not include all descendants of its last common ancestor: in this case, the more derived crocodilians and birds are excluded from "Thecodontia" as it was formerly understood. The description of the basal ornithodires Lagerpeton and Lagosuchus in the 1970s provided evidence that linked thecodonts with dinosaurs, and contributed to the disuse of the term "Thecodontia", which many cladists consider an artificial grouping.

With the identification of "crocodilian normal" and "crocodilian reversed" ankles by Sankar Chatterjee in 1978, a basal split in Archosauria was identified. Chatterjee considered these two groups to be Pseudosuchia with the "normal" ankle and Ornithosuchidae with the "reversed" ankle. Ornithosuchids were thought to be ancestral to dinosaurs at this time. In 1979, A.R.I. Cruickshank identified the basal split and thought that the crurotarsan ankle developed independently in these two groups, but in opposite ways. Cruickshank also thought that the development of these ankle types progressed in each group to allow advanced members to have semi-erect (in the case of crocodilians) or erect (in the case of dinosaurs) gaits.

Phylogeny
In many phylogenetic analyses, archosaurs have been shown to be a monophyletic grouping, thus forming a true clade. One of the first studies of archosaur phylogeny was authored by French paleontologist Jacques Gauthier in 1986. Gauthier split Archosauria into Pseudosuchia, the crocodilian line, and Ornithosuchia, the dinosaur and pterosaur line. Pseudosuchia was defined as all archosaurs more closely related to crocodiles, while Ornithosuchia was defined as all archosaurs more closely related to birds. Proterochampsids, erythrosuchids, and proterosuchids fell successively outside Archosauria in the resulting tree. Below is the cladogram from Gauthier (1986):

In 1988, paleontologists Michael Benton and J. M. Clark produced a new tree in a phylogenetic study of basal archosaurs. As in Gauthier's tree, Benton and Clark's revealed a basal split within Archosauria. They referred to the two groups as Crocodylotarsi and Ornithosuchia. Crocodylotarsi was defined as an apomorphy-based taxon based on the presence of a "crocodile-normal" ankle joint (considered to be the defining apomorphy of the clade). Gauthier's Pseudosuchia, by contrast, was a stem-based taxon. Unlike Gauthier's tree, Benton and Clark's places Euparkeria outside Ornithosuchia and outside the crown group Archosauria altogether.

The clades Crurotarsi and Ornithodira were first used together in 1990 by paleontologist Paul Sereno and A. B. Arcucci in their phylogenetic study of archosaurs. They were the first to erect the clade Crurotarsi, while Ornithodira was named by Gauthier in 1986. Crurotarsi and Ornithodira replaced Pseudosuchia and Ornithosuchia, respectively, as the monophyly of both of these clades were questioned. Sereno and Arcucci incorporated archosaur features other than ankle types in their analyses, which resulted in a different tree than previous analyses. Below is a cladogram based on Sereno (1991), which is similar to the one produced by Sereno and Arcucci:

Ornithodira and Crurotarsi are both node-based clades, meaning that they are defined to include the last common ancestor of two or more taxa and all of its descendants. Ornithodira includes the last common ancestor of pterosaurs and dinosaurs (which include birds), while Crurotarsi includes the last common ancestor of living crocodilians and three groups of Triassic archosaurs: ornithosuchids, aetosaurs, and phytosaurs. These clades are not equivalent to "bird-line" and "crocodile-line" archosaurs, which would be branch-based clades defined as all taxa more closely related to one living group (either birds or crocodiles) than the other.

Benton proposed the name Avemetatarsalia in 1999 to include all bird-line archosaurs (under his definition, all archosaurs more closely related to dinosaurs than to crocodilians). His analysis of the small Triassic archosaur Scleromochlus placed it within bird-line archosaurs but outside Ornithodira, meaning that Ornithodira was no longer equivalent to bird-line archosaurs. Below is a cladogram modified from Benton (2004) showing this phylogeny:

In Sterling Nesbitt's 2011 monograph on early archosaurs, a phylogenetic analysis found strong support for phytosaurs falling outside Archosauria. Many subsequent studies supported this phylogeny. Because Crurotarsi is defined by the inclusion of phytosaurs, the placement of phytosaurs outside Archosauria means that Crurotarsi must include all of Archosauria. Nesbitt reinstated Pseudosuchia as a clade name for crocodile-line archosaurs, using it as a stem-based taxon. Below is a cladogram modified from Nesbitt (2011):

Extinction and survival
Crocodylomorphs, pterosaurs and dinosaurs survived the Triassic–Jurassic extinction event about 200 million years ago, but other archosaurs had become extinct at or prior to the Triassic-Jurassic boundary.

Non-avian dinosaurs and pterosaurs perished in the Cretaceous–Paleogene extinction event, which occurred approximately million years ago, but crown-group birds (the only remaining dinosaur group) and many crocodyliforms survived. Both are descendants of archosaurs, and are therefore archosaurs themselves under phylogenetic taxonomy.

Crocodilians (which include all modern crocodiles, alligators, and gharials) and birds flourish today in the Holocene. It is generally agreed that birds have the most species of all terrestrial vertebrates.

Hip joints and locomotion
Like the early tetrapods, early archosaurs had a sprawling gait because their hip sockets faced sideways, and the knobs at the tops of their femurs were in line with the femur. In the early to middle Triassic, some archosaur groups developed hip joints that allowed (or required) a more erect gait. This gave them greater stamina, because it avoided Carrier's constraint, i.e. they could run and breathe easily at the same time. There were two main types of joint which allowed erect legs: It has been pointed out that an upright stance requires more energy, so it may indicate a higher metabolism and a higher body temperature.
 * The hip sockets faced sideways, but the knobs on the femurs were at right angles to the rest of the femur, which therefore pointed downwards. Dinosaurs evolved from archosaurs with this hip arrangement.
 * The hip sockets faced downwards and the knobs on the femurs were in line with the femur. This "pillar-erect" arrangement appears to have evolved independently in various archosaur lineages, for example it was common in "Rauisuchia" (non-crocodylomorph paracrocodylomorphs) and also appeared in some aetosaurs.

Diet
Most were large predators, but members of various lines diversified into other niches. Aetosaurs were herbivores and some developed extensive armor. A few crocodyliforms were herbivores, e.g., Simosuchus, Phyllodontosuchus. The large crocodyliform Stomatosuchus may have been a filter feeder. Sauropodomorphs and ornithischian dinosaurs were herbivores with diverse adaptations for feeding biomechanics.

Land, water and air
Archosaurs are mainly portrayed as land animals, but:
 * Many phytosaurs and crocodyliforms dominated the rivers and swamps and even invaded the seas (e.g., the teleosaurs, Metriorhynchidae and Dyrosauridae). The Metriorhynchidae were rather dolphin-like, with paddle-like forelimbs, a tail fluke and smooth, unarmoured skins.
 * Two clades of ornithodirans, the pterosaurs and the birds, dominated the air after becoming adapted to a volant lifestyle.
 * Some dinosaurs like Spinosaurus have been argued to have had a semiaquatic lifestyle. Hesperornithes and penguins also adapted to this lifestyle.

Metabolism
The metabolism of archosaurs is still a controversial topic. They certainly evolved from cold-blooded ancestors, and the surviving non-dinosaurian archosaurs, crocodilians, are cold-blooded. But crocodilians have some features which are normally associated with a warm-blooded metabolism because they improve the animal's oxygen supply:
 * 4-chambered hearts. Both birds and mammals have 4-chambered hearts, which completely separate the flows of oxygenated and de-oxygenated blood. Non-crocodilian reptiles have 3-chambered hearts, which are less efficient because they let the two flows mix and thus send some de-oxygenated blood out to the body instead of to the lungs. Modern crocodilians' hearts are 4-chambered, but are smaller relative to body size and run at lower pressure than those of modern birds and mammals. They also have a pulmonary bypass, which makes them functionally 3-chambered when under water, conserving oxygen.
 * a secondary palate, which allows the animal to eat and breathe at the same time.
 * a hepatic piston mechanism for pumping the lungs. This is different from the lung-pumping mechanisms of mammals and birds, but similar to what some researchers claim to have found in some dinosaurs.

Historically there has been uncertainty as to why natural selection favored the development of these features, which are very important for active warm-blooded creatures, but of little apparent use to cold-blooded aquatic ambush predators that spend the vast majority of their time floating in water or lying on river banks. Paleontological evidence shows that the ancestors of living crocodilians were active and endothermic (warm-blooded). Some experts believe that their archosaur ancestors were warm-blooded as well. This is likely because feather-like filaments evolved to cover the whole body and were capable of providing thermal insulation. Physiological, anatomical, and developmental features of the crocodilian heart support the paleontological evidence and show that the lineage reverted to ectothermy when it invaded the aquatic, ambush predator niche. Crocodilian embryos develop fully 4-chambered hearts at an early stage. Modifications to the growing heart form a pulmonary bypass shunt that includes the left aortic arch, which originates from the right ventricle, the foramen of Panizza between the left and right aortic arches, and the cog‐tooth valve at the base of the pulmonary artery. The shunt is used during diving to make the heart function as 3-chambered heart, providing the crocodilian with the neurally controlled shunting used by ectotherms. The researchers concluded that the ancestors of living crocodilians had fully 4-chambered hearts, and were therefore warm-blooded, before they reverted to a cold-blooded or ectothermic metabolism. The authors also provide other evidence for endothermy in stem archosaurs. It is reasonable to suggest that later crocodilians developed the pulmonary bypass shunt as they became cold-blooded, aquatic, and less active.

If the crocodilian ancestors and other Triassic archosaurs were warm-blooded, this would help to resolve some evolutionary puzzles:
 * The earliest crocodylomorphs, e.g., Terrestrisuchus, were slim, leggy terrestrial predators whose build suggests a fairly active lifestyle, which requires a fairly fast metabolism. And some other crurotarsan archosaurs appear to have had erect limbs, while those of rauisuchians are very poorly adapted for any other posture. Erect limbs are advantageous for active animals because they avoid Carrier's constraint, but disadvantageous for more sluggish animals because they increase the energy costs of standing up and lying down.
 * If early archosaurs were completely cold-blooded and (as seems most likely) dinosaurs were at least fairly warm-blooded, dinosaurs would have had to evolve warm-blooded metabolisms in less than half the time it took for synapsids to do the same.

Respiratory system
A recent study of the lungs of Alligator mississippiensis (the American alligator) has shown that the airflow through them is unidirectional, moving in the same direction during inhalation and exhalation. This is also seen in birds and many non-avian dinosaurs, which have air sacs to further aid in respiration. Both birds and alligators achieve unidirectional air flow through the presence of parabronchi, which are responsible for gas exchange. The study has found that in alligators, air enters through the second bronchial branch, moves through the parabronchi, and exits through the first bronchial branch. Unidirectional airflow in both birds and alligators suggests that this type of respiration was present at the base of Archosauria and retained by both dinosaurs and non-dinosaurian archosaurs, such as aetosaurs, "rauisuchians" (non-crocodylomorph paracrocodylomorphs), crocodylomorphs, and pterosaurs. The use of unidirectional airflow in the lungs of archosaurs may have given the group an advantage over synapsids, which had lungs where air moved tidally in and out through a network of bronchi that terminated in alveoli, which were cul-de-sacs. The better efficiency in gas transfer seen in archosaur lungs may have been advantageous during the times of low atmospheric oxygen which are thought to have existed during the Mesozoic.

Reproduction
Most (if not all) archosaurs are oviparous. Birds and crocodilians lay hard-shelled eggs, as did extinct dinosaurs, and crocodylomorphs. Hard-shelled eggs are present in both dinosaurs and crocodilians, which has been used as an explanation for the absence of viviparity or ovoviviparity in archosaurs. However, both pterosaurs and baurusuchids have soft-shelled eggs, implying that hard shells are not a plesiomorphic condition. The pelvic anatomy of Cricosaurus and other metriorhynchids and fossilized embryos belonging to the non-archosaur archosauromorph Dinocephalosaurus, together suggest that the lack of viviparity among archosaurs may be a consequence of lineage-specific restrictions.

Archosaurs are ancestrally superprecocial as evidenced in various dinosaurs, pterosaurs, and crocodylomorphs. However, parental care did evolve independently multiple times in crocodilians, dinosaurs, and aetosaurs. In most such species the animals bury their eggs and rely on temperature-dependent sex determination. The notable exception are Neornithes which incubate their eggs and rely on genetic sex determination – a trait that might have given them a survival advantage over other dinosaurs.

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/

title: Archosaur


text:
Ryōtarō Shiba

Teiichi Fukuda (福田 定一), also known as Ryōtarō Shiba (司馬 遼太郎), was a Japanese author. He is best known for his novels about historical events in Japan and on the Northeast Asian sub-continent, as well as his historical and cultural essays pertaining to Japan and its relationship to the rest of the world.

Career
Shiba took his pen name from Sima Qian, the great Han dynasty historian (Shiba is the Japanese rendition of Sima). He studied Mongolian at the Osaka School of Foreign Languages (now the School of Foreign Studies at Osaka University) and began his career as a journalist with the Sankei Shimbun, one of Japan's major newspapers. After World War II Shiba began writing historical novels. The magazine Shukan Asahi (ja:週刊朝日) printed Shiba's articles about his travels within Japan in a series that ran for 1,146 installments. Shiba received the Naoki Prize for the 1959 novel Fukurō no Shiro ("Castle of Owls"). In 1993 Shiba received the Government's Order of Cultural Merit. Shiba was a prolific author who frequently wrote about the dramatic change Japan went through during the late Edo and early Meiji periods. His most monumental works include Kunitori Monogatari, Ryoma ga Yuku (see below), Moeyo Ken, and Saka no Ue no Kumo, all of which have spawned dramatizations, most notably Taiga dramas aired in hour-long segments over a full year on NHK television. He also wrote numerous essays that were published in collections, one of which—Kaidō wo Yuku—is a multi-volume journal-like work covering his travels across Japan and around the world. Shiba is widely appreciated for the originality of his analyses of historical events, and many people in Japan have read at least one of his works.

Several of Shiba's works have been translated into English, including  Drunk as a Lord: Samurai Stories  (2001), his fictionalized biographies of Kukai (Kukai the Universal: Scenes from His Life, 2003) and Tokugawa Yoshinobu (The Last Shogun: The Life of Tokugawa Yoshinobu, 2004), as well as  The Tatar Whirlwind: A Novel of Seventeenth-Century East Asia (2007) and  Clouds Above the Hill  (2012, 2013, 2014).

Ryōma Goes His Way
One of Shiba's best known works, Ryōma Goes His Way (竜馬がゆく), is a historical novel about Sakamoto Ryōma, a samurai who was instrumental in bringing about Japan's Meiji Restoration, after which values and elements from Western culture were introduced into the country, sparking dramatic change. The late Edo period was a very confused time when the country split into two factions. Japan had banned international trade for over two hundred years and isolated itself from the rest of the world. During the Edo period, the Japanese government, which was led by the Tokugawa clan, had agreed to open the country to trade with the United States and several European countries. However, many people were against this and they started a movement called Sonnō-Jōi (revere the emperor and expel the barbarians). They believed that they should stand up and fight the foreigners to protect the country from outside domination. The Tokugawa had usurped political power from the emperor, but he was still considered by many to be the sacred symbol of Japan. To protect the country, the Sonnō-Jōi faction sought to restore the emperor's political authority by overthrowing the Tokugawa shogunate. Partisans of these two political institutions caused civil war-like confusion, and assassinations were frequent.

In Ryōma ga Yuku, Sakamoto Ryōma, the protagonist, starts out as a member of the Sonnō-Jōi faction but gradually realizes that people need to realize how much stronger other countries have grown during Japan's two centuries of national seclusion. Japan was almost powerless in the face of the technology and well-developed industry of the contemporary Western powers. He believed that Japan needed to adopt elements of Western culture to develop into a country that could stand equally among nations.

Sakamoto Ryōma was not well known in Japan prior to the publication of Ryōma ga Yuku. Ryōma ga Yuku is Shiba's best selling work in Japanese, with 21,250,000 copies sold.

Kaidō wo Yuku
Kaidō wo Yuku (街道をゆく) is a series of travel essays initially published in Shūkan Asahi, a weekly magazine, from 1971 until 1996. Shiba wrote the series with an intercultural perspective, making observations about the history, geography, and people of the places he visited. Though mostly about different areas of Japan, the series includes several volumes on foreign lands as well—China, Korea, the Namban countries (Spain and Portugal), Ireland, the Netherlands, Mongolia, Taiwan, and New York.

The work, now available in multi-volume book form, was also developed into documentary series and broadcast on NHK, Japan's public television broadcaster.

The series ran for 1,146 installments.

Clouds Above the Hill
Another well-known work, Clouds Above the Hill (坂の上の雲), is a historical epic centering on the careers of two ambitious brothers who work their way up from a rural backwater to positions of eminence in the new post-1868 Meiji period. In it, the Akiyama brothers strive to build a Japanese military capable of holding its own in an unstable region and the Russo-Japanese War becomes the central stage for their involvement in the frenzied modernisation and ascendancy of Japan in the region and subsequently, the world. It is Shiba's second best selling work in Japanese, with 14,750,000 copies sold.

Battles of Khalkhin Gol
Shiba began working on a novel based on the Battles of Khalkhin Gol and conducted research. However, as he delved deeper into his research, his motivation to write dwindled.

"'I started hating being Japanese.' 'I can't understand this country Japan, which engages in such foolish acts.'"

In the end, he gave up writing.

Death
Shiba suffered internal bleeding and lapsed into a coma on February 10, 1996. He died two days later.

Novels

 * Fukurō no Shiro (1959)
 * Zeeroku Bushido (上方武士道, 1960)
 * Kaze no Bushi (1961)
 * Senun no yume (戦雲の夢, 1961)
 * Fujin no mon (風神の門, 1962)
 * Ryoma ga Yuku (竜馬がゆく, 1963–66)
 * Moeyo Ken (1964)
 * Shirikurae Magoichi (尻啖え孫市, 1964)
 * Komyo ga tsuji (功名が辻, 1965)
 * Shiro wo toru hanashi (城をとる話, 1965)
 * Kunitori monogatari (国盗り物語, 1965)
 * Yotte soro (酔って候, 1965), published in English as Drunk as a Lord
 * Hokuto no hito (北斗の人, 1966)
 * Niwaka Naniwa yukyoden (俄 浪華遊侠伝, 1966)
 * Sekigahara (関ヶ原, 1966)
 * Jūichibanme no shishi (十一番目の志士, 1967)
 * Saigo no Shōgun (最後の将軍, 1967), translated into English as The Last Shogun: The Life of Tokugawa Yoshinobu , (ISBN 1568363567) about Tokugawa Yoshinobu.
 * Junshi (殉死, 1967)
 * Natsukusa no fu (夏草の賦, 1968)
 * Shinshi taikoki (新史太閤記, 1968)
 * Yoshitsune (義経, 1968)
 * Touge (峠, 1968)
 * Musashi (武蔵, 1968)
 * Saka no ue no kumo (1969), translated into English as  Clouds Above the Hill  (ISBN 1138911968), a work of historical fiction about the Russo-Japanese War.
 * Yōkai (妖怪, 1969)
 * Daitōzenshi (大盗禅師, 1969)
 * Saigetsu (歳月, 1969)
 * Yoni sumu hibi (世に棲む日日, 1971)
 * Jousai (城塞, 1971–72)
 * Kashin (花神, 1972)
 * Haō no ie (覇王の家, 1973)
 * Harimanada monogatari (播磨灘物語, 1975)
 * Tobu ga gotoku (翔ぶが如く, 1975–76)
 * Kūkai no fukei (空海の風景, 1975), translated into English as  Kukai the Universal: Scenes from his Life  (ISBN 4925080474) about the great Japanese monk Kukai who founded the Shingon school and is said to have invented the Japanese kana writing system.
 * Kochō no yume (胡蝶の夢, 1979)
 * Kouu to Ryūhō (項羽と劉邦, 1980)
 * Hitobito no ashioto (ひとびとの跫音, 1981)
 * Nanohana no oki (菜の花の沖, 1982)
 * Hakone no saka (箱根の坂, 1984)
 * Dattan shippuroku (韃靼疾風録, 1987), translated into English as  The Tatar Whirlwind: A Novel of Seventeenth-Century East Asia  (ISBN 1891640461), about the decline of the Ming dynasty, the rise of the Manchus and the interplay of these two periods in China's history with Tokugawa Japan.

Manga

 * Moeyo Ken (2021–present) (written by Emeru Komatsu and illustrated by Yoshiki Kanata; serialized on Comic Bunch Kai)
 * Ryōma ga Yuku (2022–present) (illustrated by Yū Suzunoki; serialized on Shūkan Bunshun)

Honours

 * Naoki Prize (1960)
 * Kikuchi Kan Prize (1966)
 * Yomiuri Prize (1981)
 * Asahi Prize (1982)
 * Person of Cultural Merit (1991)
 * Order of Culture (1993)
 * Junior Third Rank (1996, Posthumous)

title: Ryōtarō Shiba


text:
Photorespiration

Photorespiration (also known as the oxidative photosynthetic carbon cycle or C2 cycle) refers to a process in plant metabolism where the enzyme RuBisCO oxygenates RuBP, wasting some of the energy produced by photosynthesis. The desired reaction is the addition of carbon dioxide to RuBP (carboxylation), a key step in the Calvin–Benson cycle, but approximately 25% of reactions by RuBisCO instead add oxygen to RuBP (oxygenation), creating a product that cannot be used within the Calvin–Benson cycle. This process lowers the efficiency of photosynthesis, potentially lowering photosynthetic output by 25% in plants. Photorespiration involves a complex network of enzyme reactions that exchange metabolites between chloroplasts, leaf peroxisomes and mitochondria.

The oxygenation reaction of RuBisCO is a wasteful process because 3-phosphoglycerate is created at a lower rate and higher metabolic cost compared with RuBP carboxylase activity. While photorespiratory carbon cycling results in the formation of G3P eventually, around 25% of carbon fixed by photorespiration is re-released as and nitrogen, as ammonia. Ammonia must then be detoxified at a substantial cost to the cell. Photorespiration also incurs a direct cost of one ATP and one NAD(P)H.

While it is common to refer to the entire process as photorespiration, technically the term refers only to the metabolic network which acts to rescue the products of the oxygenation reaction (phosphoglycolate).

Photorespiratory reactions
Addition of molecular oxygen to ribulose-1,5-bisphosphate produces 3-phosphoglycerate (PGA) and 2-phosphoglycolate (2PG, or PG). PGA is the normal product of carboxylation, and productively enters the Calvin cycle. Phosphoglycolate, however, inhibits certain enzymes involved in photosynthetic carbon fixation (hence is often said to be an 'inhibitor of photosynthesis'). It is also relatively difficult to recycle: in higher plants it is salvaged by a series of reactions in the peroxisome, mitochondria, and again in the peroxisome where it is converted into glycerate. Glycerate reenters the chloroplast and by the same transporter that exports glycolate. A cost of 1 ATP is associated with conversion to 3-phosphoglycerate (PGA) (Phosphorylation), within the chloroplast, which is then free to re-enter the Calvin cycle.

Several costs are associated with this metabolic pathway; the production of hydrogen peroxide in the peroxisome (associated with the conversion of glycolate to glyoxylate). Hydrogen peroxide is a dangerously strong oxidant which must be immediately split into water and oxygen by the enzyme catalase. The conversion of 2× 2Carbon glycine to 1× serine in the mitochondria by the enzyme glycine-decarboxylase is a key step, which releases, NH3, and reduces NAD to NADH. Thus, one molecule is produced for every two molecules of  (two deriving from RuBisCO and one from peroxisomal oxidations). The assimilation of NH3 occurs via the GS-GOGAT cycle, at a cost of one ATP and one NADPH.

Cyanobacteria have three possible pathways through which they can metabolise 2-phosphoglycolate. They are unable to grow if all three pathways are knocked out, despite having a carbon concentrating mechanism that should dramatically lower the rate of photorespiration (see below).

Substrate specificity of RuBisCO

The oxidative photosynthetic carbon cycle reaction is catalyzed by RuBP oxygenase activity:

 * RuBP + → Phosphoglycolate + 3-phosphoglycerate + 2

During the catalysis by RuBisCO, an 'activated' intermediate is formed (an enediol intermediate) in the RuBisCO active site. This intermediate is able to react with either or. It has been demonstrated that the specific shape of the RuBisCO active site acts to encourage reactions with. Although there is a significant "failure" rate (~25% of reactions are oxygenation rather than carboxylation), this represents significant favouring of, when the relative abundance of the two gases is taken into account: in the current atmosphere, is approximately 500 times more abundant, and in solution  is 25 times more abundant than.

The ability of RuBisCO to specify between the two gases is known as its selectivity factor (or Srel), and it varies between species, with angiosperms more efficient than other plants, but with little variation among the vascular plants.

A suggested explanation of RuBisCO's inability to discriminate completely between and  is that it is an evolutionary relic: The early atmosphere in which primitive plants originated contained very little oxygen, the early evolution of RuBisCO was not influenced by its ability to discriminate between  and.

Conditions which affect photorespiration
Photorespiration rates are affected by:

Altered substrate availability: lowered or increased O2
Factors which influence this include the atmospheric abundance of the two gases, the supply of the gases to the site of fixation (i.e. in land plants: whether the stomata are open or closed), the length of the liquid phase (how far these gases have to diffuse through water in order to reach the reaction site). For example, when the stomata are closed to prevent water loss during drought: this limits the supply, while  production within the leaf will continue. In algae (and plants which photosynthesise underwater); gases have to diffuse significant distances through water, which results in a decrease in the availability of relative to. It has been predicted that the increase in ambient concentrations predicted over the next 100 years may lower the rate of photorespiration in most plants by around 50%. However, at temperatures higher than the photosynthetic thermal optimum, the increases in turnover rate are not translated into increased assimilation because of the decreased affinity of Rubisco for.

Increased temperature
At higher temperatures RuBisCO is less able to discriminate between and. This is because the enediol intermediate is less stable. Increasing temperatures also lower the solubility of, thus lowering the concentration of relative to  in the chloroplast.

Biological adaptation to minimize photorespiration

The vast majority of plants are C3, meaning they photorespire when necessary. Certain species of plants or algae have mechanisms to lower the uptake of molecular oxygen by RuBisCO. These are commonly referred to as Carbon Concentrating Mechanisms (CCMs), as they increase the concentration of so that RuBisCO is less likely to produce glycolate through reaction with.

Biochemical carbon concentrating mechanisms
Biochemical CCMs concentrate carbon dioxide in one temporal or spatial region, through metabolite exchange. C4 and CAM photosynthesis both use the enzyme Phosphoenolpyruvate carboxylase (PEPC) to add to a 4-carbon sugar. PEPC is faster than RuBisCO, and more selective for.

C4
C4 plants capture carbon dioxide in their mesophyll cells (using an enzyme called phosphoenolpyruvate carboxylase which catalyzes the combination of carbon dioxide with a compound called phosphoenolpyruvate (PEP)), forming oxaloacetate. This oxaloacetate is then converted to malate and is transported into the bundle sheath cells (site of carbon dioxide fixation by RuBisCO) where oxygen concentration is low to avoid photorespiration. Here, carbon dioxide is removed from the malate and combined with RuBP by RuBisCO in the usual way, and the Calvin cycle proceeds as normal. The concentrations in the Bundle Sheath are approximately 10–20 fold higher than the concentration in the mesophyll cells.

This ability to avoid photorespiration makes these plants more hardy than other plants in dry and hot environments, wherein stomata are closed and internal carbon dioxide levels are low. Under these conditions, photorespiration does occur in C4 plants, but at a much lower level compared with C3 plants in the same conditions. C4 plants include sugar cane, corn (maize), and sorghum.

CAM (Crassulacean acid metabolism)
CAM plants, such as cacti and succulent plants, also use the enzyme PEP carboxylase to capture carbon dioxide, but only at night. Crassulacean acid metabolism allows plants to conduct most of their gas exchange in the cooler night-time air, sequestering carbon in 4-carbon sugars which can be released to the photosynthesizing cells during the day. This allows CAM plants to minimize water loss (transpiration) by maintaining closed stomata during the day. CAM plants usually display other water-saving characteristics, such as thick cuticles, stomata with small apertures, and typically lose around 1/3 of the amount of water per fixed.

C2
C2 photosynthesis (also called glycine shuttle and photorespiratory CO2 pump) is a CCM that works by making use of – as opposed to avoiding – photorespiration. It performs carbon refixation by delaying the breakdown of photorespired glycine, so that the molecule is shuttled from the mesophyll into the bundle sheath. Once there, the glycine is decarboxylated in mitochondria as usual, releasing CO2 and concentrating it to triple the usual concentration.

Although C2 photosynthesis is traditionally understood as an intermediate step between C3 and C4, a wide variety of plant lineages do end up in the C2 stage without further evolving, showing that it is an evolutionary steady state of its own. C2 may be easier to engineer into crops, as the phenotype requires fewer anatomical changes to produce.

Algae
There have been some reports of algae operating a biochemical CCM: shuttling metabolites within single cells to concentrate in one area. This process is not fully understood.

Biophysical carbon-concentrating mechanisms
This type of carbon-concentrating mechanism (CCM) relies on a contained compartment within the cell into which is shuttled, and where RuBisCO is highly expressed. In many species, biophysical CCMs are only induced under low carbon dioxide concentrations. Biophysical CCMs are more evolutionary ancient than biochemical CCMs. There is some debate as to when biophysical CCMs first evolved, but it is likely to have been during a period of low carbon dioxide, after the Great Oxygenation Event (2.4 billion years ago). Low periods occurred around 750, 650, and 320–270 million years ago.

Eukaryotic algae
In nearly all species of eukaryotic algae (Chloromonas being one notable exception), upon induction of the CCM, ~95% of RuBisCO is densely packed into a single subcellular compartment: the pyrenoid. Carbon dioxide is concentrated in this compartment using a combination of CO2 pumps, bicarbonate pumps, and carbonic anhydrases. The pyrenoid is not a membrane-bound compartment but is found within the chloroplast, often surrounded by a starch sheath (which is not thought to serve a function in the CCM).

Hornworts
Certain species of hornwort are the only land plants that are known to have a biophysical CCM involving concentration of carbon dioxide within pyrenoids in their chloroplasts.

Cyanobacteria
Cyanobacterial CCMs are similar in principle to those found in eukaryotic algae and hornworts, but the compartment into which carbon dioxide is concentrated has several structural differences. Instead of the pyrenoid, cyanobacteria contain carboxysomes, which have a protein shell, and linker proteins packing RuBisCO inside with a very regular structure. Cyanobacterial CCMs are much better understood than those found in eukaryotes, partly due to the ease of genetic manipulation of prokaryotes.

Possible purpose of photorespiration
Lowering photorespiration may not result in increased growth rates for plants. Photorespiration may be necessary for the assimilation of nitrate from soil. Thus, a lowering in photorespiration by genetic engineering or because of increasing atmospheric carbon dioxide may not benefit plants as has been proposed. Several physiological processes may be responsible for linking photorespiration and nitrogen assimilation. Photorespiration increases availability of NADH, which is required for the conversion of nitrate to nitrite. Certain nitrite transporters also transport bicarbonate, and elevated has been shown to suppress nitrite transport into chloroplasts. However, in an agricultural setting, replacing the native photorespiration pathway with an engineered synthetic pathway to metabolize glycolate in the chloroplast resulted in a 40 percent increase in crop growth.

Although photorespiration is much lower in C4 species, it is still an essential pathway – mutants without functioning 2-phosphoglycolate metabolism cannot grow in normal conditions. One mutant was shown to rapidly accumulate glycolate.

Although the functions of photorespiration remain controversial, it is widely accepted that this pathway influences a wide range of processes from bioenergetics, photosystem II function, and carbon metabolism to nitrogen assimilation and respiration. The oxygenase reaction of RuBisCO may prevent depletion near its active sites and contributes to the regulation of CO2. concentration in the atmosphere The photorespiratory pathway is a major source of hydrogen peroxide in photosynthetic cells. Through production and pyrimidine nucleotide interactions, photorespiration makes a key contribution to cellular redox homeostasis. In so doing, it influences multiple signalling pathways, in particular, those that govern plant hormonal responses controlling growth, environmental and defense responses, and programmed cell death.

It has been postulated that photorespiration may function as a "safety valve", preventing the excess of reductive potential coming from an overreduced NADPH-pool from reacting with oxygen and producing free radicals (oxidants), as these can damage the metabolic functions of the cell by subsequent oxidation of membrane lipids, proteins or nucleotides. The mutants deficient in photorespiratory enzymes are characterized by a high redox level in the cell, impaired stomatal regulation, and accumulation of formate.

title: Photorespiration