Art of arrangement of organisms into groups (taxa) on the basis of relationships

Charles Darwin, in Origin of Species, 1859

• taxonomy : the orderly classification of organisms into appropriate categories (taxa) on the basis of relationships among them, with the application of suitable and correct names.
• numerical taxonomy / adansonian or numerical classification : an arithmetic method of classifying large numbers of bacterial strains on the basis of their overall similarity to one another, according to the number of phenotypic characters they share, each character being given equal weight
• taxon : a particular group (category) into which related organisms are classified; the main categories are (in descending order):
• kingdom : classically, one of the 3 categories into which natural objects are usually classified:
• the animal kingdom, including all animals;
• the plant kingdom, including all plants;
• the mineral kingdom, including all objects and substance without life.
• a fourth kingdom, the Protista, has been added and includes all single-celled organisms
• phylum : a primary or main division of a kingdom, composed of a group of related classes; in the taxonomy of plants, the term division is used instead.
• division : in the taxonomy of plants, a primary grouping composed of classes; the equivalent of phylum in the animal kingdom. In the taxonomy of fungi, former term for phylum.
• subphylum : a taxonomic category sometimes established, subordinate to a phylum and superior to a class.
• subdivision : in the classification of plants and fungi, a taxonomic category inferior to a division but superior to a class; equivalent to the subphylum of animal taxonomy.
• class : a taxonomic category subordinate to a phylum (or subphylum) and superior to an order
• form-class : an artificial taxonomic category comparable to a class, to which organisms are provisionally assigned, as are imperfect fungi until their perfect (sexual) stages are identified. Form-classes are subdivided into form-orders, form-families, and so on.
• order : a taxonomic category subordinate to a class and superior to a family
• suborder : a taxonomic category sometimes established, subordinate to an order and superior to a family
• family : a taxonomic subdivision subordinate to an order (or suborder) and superior to a tribe (or subfamily)
• subfamily : a taxonomic category sometimes established, subordinate to a family and superior to a tribe or genus
• tribe : a taxonomic category subordinate to a family (or subfamily) and superior to a genus (or subtribe)
• subtribe : a taxonomic category sometimes established, subordinate to a tribe and superior to a genus
• genus : a taxonomic category subordinate to a tribe (or subtribe) and superior to a species (or subgenus).
• subgenus : a taxonomic category between a genus and a species.
• species : a taxonomic category subordinate to a genus (or subgenus), and superior to a subspecies or variety, composed of individuals possessing common characters distinguishing them from other categories of individuals of the same taxonomic level. In taxonomic nomenclature, species are designated by the genus name followed by a Latin or latinized adjective or noun.
• genospecies : a group of interfertile strains (definition appliable only to sexually-reproducing species)
• taxospecies : a group of strains with high phenetic similitude (Adanson taxonomy)
• nominal species : a group of strains with no common features
• type species : in bacteriology, the species that characterizes a genus, usually the first species validly described in the genus, but it may be one arbitrarily designated as such for classification purposes.
• subspecies : a taxonomic category subordinate to a species, whose members differ morphologically from other members of the species but remain capable of interbreeding with them; a variety or race.
• type / variant (-var) / intraspecies :
• phenotypic variation : the total range of variation, of whatever cause, observed in one character.
• continuous variation : phenotypic differences so numerous and minute that the values selected for observation form a continuous spectrum, and no one phenotype or group of phenotypes predominates
• quasicontinuous variation : variation in which the underlying distribution of variability is continuous but a threshold effect makes it appear discontinuous
• discontinuous variation : phenotypic differences that are marked, do not grade into one another, and form two or more separate, discontinuous classes.
• genotype / genovar / genomovar = organisms differentiated on the basis of the genome composition
• ribotype : organims differentiated on the basis of rDNA.
Multilocus sequence typing (MLST) uses allelic variation in housekeeping genes to characterize isolates
• serotype / serovar : organisms differentiated on the basis of the antibodies which recognize them
• zymodeme : different types with same enzyme electrophoretic mobility
• pathotype / pathovar : organisms differentiated on the basis of the pathogenetics of the disease they induce
• auxotype / biotype / biovar (bv.) / biovariant : organisms differentiated on the basis of environmental conditions required for growth.
• chemovar :
• phagotype / phage type : an intraspecies type of bacterium demonstrated on the basis of phage typing (characterization of bacteria, extending to strain differences, by demonstration of susceptibility to one or more (a spectrum) races of bacteriophage; widely applied to staphylococci, typhoid bacilli, etc., for epidemiological purposes)
• antibiotype : organism differentiated on the basis of the sensivity to antibiotics (antibiogram)
• phylogeny : the complete developmental history of a race or group of animals
• morphophyly : the branch of phylogenesis dealing with the evolutionary development of form
The eukaryotic genome resulted from a fusion of 2 diverse prokaryotic genomes, and therefore at the deepest levels linking prokaryotes and eukaryotes, the tree of life is actually a ring of life. One fusion partner branches from deep within an ancient photosynthetic clade, and the other is related to the archaeal prokaryotes. The eubacterial organism is either a proteobacterium, or a member of a larger photosynthetic clade that includes the Cyanobacteria and the Proteobacteriaref.
• binomial or linnaean nomenclature : the nomenclature used in scientific classification of living organisms in which each organism is designated by 2 latinized names (genus (nominative case) and species (conjugated adjective or genitive case)), both of which must always be used because species names are not necessarily unique. NOTE: The genus name is always capitalized, the species name is not, and both are italicized, e.g., Escherichia coli. When a name is repeated the genus name may be abbreviated by its initial, e.g., E. coli.
• author or authority : in some taxonomic disciplines, the scientific name is not considered complete unless the name of the taxon is followed by the name(s) of the person(s) who formally described it. Authorities have standardized abbreviations; for example, 'L.'is the abbreviation for the Swedish naturalist Carl Linnaeus
• 1753 : Species Plantarum
• 1758 : Systema Naturae extended two-part names to animals
For examples of the intricacies of authority citations, see Article 46 of the International Code of Botanical Nomenclature (St. Louis Code).
• PhyloCode system names organisms according to their evolutionary relationships.
• last universal common ancestor (LUCA) / progenote: most researchers now believe we should think at LUCA not as a single organism but as a pool of genes shared among a host of primitive organisms. Mutations build up and overwrite one another over such a span of time, erasing the phylogenetic signal. Also, phylogenetic analysis has some statistical quirks : for example, the gene sequences that evolve most quickly tend to come together on tress, even if they are only distantly related. A recent study based on slowly evolving sequences placed a non-thermophilic group at the base of the bacterial family tree. Phylogenetic evidence points to thermophiles as the progenote. Either life arose in a hydrothermal vent (underwater geysers with pH 3-8 and 400°C), or only thermophiles were able to survive the last of the major impacts during the late bombardment period. But so far the results have been split. One reconstruction of a putative ribosomal RNA sequence for LUCA suggests that it was a cool-water creature. But this analysis omitted some thermophilic groups : there is a trend towards lower G-C ratios as one moves up the tree of life, showing that LUCA was a thermophile. Extensive comparison of genome sequences from widely diveergent organisms has identified only about 60 genes that appear to be universal, and therefore probably date back to LUCA : that's nowhere enough to sustain an organism. The majority of these genes are involved in translation. There's nothing for a cell membrane, or for energy metabolism, or any synthetic capabilities. There should have been several times more genes. At the same time, evidence is mounting that early life forms were particularly promiscuous in sharing their genes around, in a process called horizontal transfer. Among the genes that should be highly conserved - and therefore good for phylogenies - are those involved in handling genetic information, such as DNA polymerase, which copies DNA, and topoisomerase, which controls the structure of DNA. But the surprise result from this work was that the patterns of ancestry vary depending on which gene you look atref. In other words, the phylogenies revealed only the ancestry of the genes themselves, not the relatedness of the species that housed them. This showed genes had hopped between lineages. Some biologists believe that horizontal gene transfer makes LUCA unknowable as 4 billion years is plenty of time to scramble the phylogenetic record. But while trees vary from gene to gene, the average tree that emerges from comparing many genes at once is consistent with the results obtained for ribosomal RNA alone. In 1998, the puzzles surrounding the nature of the first life forms led Woese to propose that the universal common ancestor was actually a community of organisms sharing genesref. In this communal world, the various primordial organisms had indipendently come up with solutions to similar problems, such as how to build and expand a membrane, or how to convert organic molecules into useful energy. Ultimately, around 3.5 billion years ago, the modern domains of life would have emerged from the gene-swapping melée with many of the genes from the last common community riding on their coar-tails. Inheritance and mutation would then have replaced gene transfer as the most important source of biological novelty as cells became more complex and their functions became less interchangeable. This point was the true origin of species, the darwinian thresholdref. Contemporary genomes tell us the mininum number of genes needed by a self-sufficient organism is about 600.

New findings are backing up a theory that life originated in ice. If it�s true, it could boost the chances that life might turn up in places considerably colder than our planet. Ice might have been an ideal environment for the first self-replicating molecules. The theory departs from mainstream thinking on the origins of life, which usually assumes a warm, or hot, and wet environment was necessary. Conditions associated with freezing, rather than �warm and wet� conditions, could have been of key importance for the chemical reactions that led to liferef. Ice might have been a favorable environment to generate the first self-replicating molecules, a precondition for life. These molecules would be of a type called ribonucleic acids, or RNA�a chemical cousin of DNA, which makes up genes. Many researchers believe the first self-replicating molecule was RNA, not DNA. This is because RNA can do various things in addition to carrying genetic information, which is all that DNA basically does. Some of RNA�s activities seem to be similar to what would be required for self-replication, something that DNA can�t do, strictly speaking. DNA needs the help of other molecules to copy itself. Also, RNA still exists in living cells, where it has various functions�some so basic to life that many scientists think RNA must have been there from the beginning. The theory that RNA started it all, a 20-year-old proposal called the �RNA world hypothesis,� holds that RNA was not only the first self-replicating molecule, but also that it initially carried out most of life�s functions, such as metabolism and cell formation. Most biologists consider the RNA world hypothesis at least plausible, but it has some problems. It�s not easy to explain how the first self-replicating RNA molecules might have arisen. RNA molecules tend to fall apart under warm conditions outside of cells. This would prevent the buildup of the rather long, complex RNA molecules that would probably be needed to conduct life processes. Various conditions can prevent RNA molecules� breakdown. These include various types of water solutions, and freezing. But freezing may have been the one that most likely occurred on the early Earth. Freezing usually slows down chemical reactions, which is why cold places are generally considered hostile to life. But freezing actually speeds up some of RNA�s key activities. This is because ice contains hard, tiny compartments that hold the molecules in one place, where they can react together. Some of these reactions result in the creation of bigger RNA molecules. In liquid water, by contrast, the molecules don�t come close enough together often enough to react as much. Thus they tend to fall apart faster than they can react to create bigger products. In essence, the small compartments in ice play the role that cells today play in bringing the molecules together to react, Landweber and her colleagues argue. Dehydrated substances�a sort of primordial sludge, for instance�could also have provided a function similar to ice, they added, but ice works better.  Landweber�s group conducted an experiment to test the theory. The researchers broke to pieces some RNA molecules found in normal cells. This process yielded more, smaller, RNA molecules. By doing this, the researchers produced RNA molecules of sizes that biologists think might have been available on early Earth. They then experimented to find out what sort of capabilities these smaller RNAs had. The broken-up RNAs still could carry out some of the same functions as normal RNAs, but only in ice or sometimes other extreme conditions, such as dehydration. These activities included grabbing other pieces of RNA and attaching them together, an activity called �ligation� that is similar to self-replication. To fully self-replicate, a molecule must attach other molecules together in such a way as to match the sequence of chemical pieces that characterize the first molecule. This process is called �template-directed� ligation. But the ligation alone�even without the self-replication�can build up ever larger and more complex RNA molecules, which according to the RNA world hypothesis could eventually develop self-replicating abilities. The theory that an icy environment might have helped jump-start life isn�t new. Researchers proposed in 1994, for example, that repeated cycles of freezing and thawing could help accelerate some of the chemical reactions necessary for life. Such a scenario might have existed on early Earth, where according to some researchers, repeated meteor and comet impacts might have periodically melted an otherwise icy environment. However, Landweber and her team seem to be the first to have provided an account of how the �RNA world� might have fit into this scenario.  Although freeze-thaw cycles are helpful for the processes they describe, such cycles aren�t strictly necessary in their proposal. Moreover, it is worth noting that Jupiter�s moon Europa and even Mars are also thought to contain large amounts of liquid water and ice now or at some time in the past.� The possibility of RNA activities in ice, lends some credibility to claims that the rather extreme environments of these extraterrestrial locations could have provided suitable conditions for the emergence of life.  However, the origin of life and the RNA world aren�t necessarily the same thing. The RNA world as complex self-replicating molecular society could appear at multiple places in Universe, but not necessarily result in the appearance of life as we know it. This transition may actually be rare. I also think that Earth is a possible but not necessarily the best place where the RNA world could start. Rather, I would bet on Europa or a giant comet. If the transition to life as we know it did occur, it could spread across many planets through cross-contamination, carried by comets or meteoritesref (May 25, 2004 issue of the journal Nucleic Acids Research)
• carbonaceous compounds found in sedimentary rocks in Buck Reef Chert in South Africa�one of the oldest sedimentary areas in the world- were laid down by mats of photosynthetic organisms living in shallow seas 3,416-Myr years ago, and not abiotic hydrothermal processes. Chert is a microcrystalline form of quartz and in the pictures, all the white stuff you see is chert. All the black stuff you see is carbonaceous mineral which is organic matter produced by organisms and which has since been heated to such a degree and for a long enough time that it's now approaching graphite. They found laminations only in rocks deposited in underwater depths between 15 and 200 meters, which in the modern ocean is about the depth that light can penetrate. In addition, the carbon isotope composition of the carbonaceous matter was found to be 3.5% to 2% less carbon-13 to carbon-12 compared with a standard value found in plain rock, consistent with fixation by the biological Calvin cycle process. Organic matter formed in hydrothermal vents can also have that composition, but tends to be present among other compositions as wellref
• the most recent common ancestor (MRCA) of all humanity, from whom everyone alive today is directly descended, probably lived around 1,500 BC in eastern Asia. If it were not for the fact that oceans helped to keep populations apart, the human race would have mingled even more freely, the researchers argue. This model relies on the assumption that no population has remained completely isolated for any significant length of time : even Tasmania, once thought to be isolated by choppy seas, contains no people with purely Tasmanian blood. Looking at the whole sweep of the Americas, Europe, Asia, right across to Japan, I wouldn't be surprised if we had a common ancestor in the AD years. In 5,400 BC everyone alive was either an ancestor of all of humanity, or of nobody alive today. The researchers call this the 'identical ancestors' point: the time before which all the family trees of people today are composed of exactly the same individualsref. Human�chimpanzee genetic divergence varies from < 84% to > 147% of the average, a range of more than 4 million years. Our analysis also shows that human�chimpanzee speciation occurred < 6.3 million years ago and probably more recently, conflicting with some interpretations of ancient fossils. Most strikingly, chromosome X shows an extremely young genetic divergence time, close to the genome minimum along nearly its entire length. These unexpected features would be explained if the human and chimpanzee lineages initially diverged, then later exchanged genes before separating permanentlyref.
• molecular clock : the rate of change in mtDNA was first calculated for vertebrates, using fossil vertebrates to calibrate the scale, but it then turned out that evolution progresses at a different rate in different groups of organisms, so the vertebrate rate gave wacky dates when applied to anything else. And it was not clear how constant the rate of mutation was over time for any group. Worse, dates given by the molecular clock consistently disagreed with the fossil record, tending to give estimates that were much older, by as much as several hundred million years. A new 'relaxed' molecular clock allows for different rates of mutation in different groups of species. They used 36 diverse living species to create an evolutionary tree that included all the major groups of organisms, then tied it to the fossil record at 6 points. That is, for 5 ancient creatures, the researchers made sure that the dates stayed within a range determined by conventional dating of the fossils. The rest of the tree would have to fit with these six knowns. Then the researchers looked at > 100 essential proteins in each of the 36 living species : over long periods of time, small mutations in the organisms' DNA make the proteins' sequences drift apart. The researchers used the differences between the species to estimate how fast the mutation rate is in each group. Finally, they used a computer model to fit the different mutation rates to their tree, together with the dates from the six fossils. Here and there, species show up in the tree before they do in the fossil record. But this makes sense because a fossil may have formed quite a bit later than the first appearance of that speciesref.
• How to make a �mineral fungus' : to make the cells appear, place a compressed pellet of 0.2 g powdered CaCl2 into about 250 mL of a 1.5 M NaHCO3 solution. The cell grows to a diameter of about 1 cm over 1 hour. To stimulate 'metabolic' reactions inside the cell, make a similar compressed pellet from 186 mg of CaCl2 and 14 mg of CuCl2. Add 2.3 mL of 30% aqueous H2O2 to 250 mL of a 1.5 M NaHCO3 solution to produce a 0.08 M H2O2 solution. Dissolve 3 g of NaI into the solution, and then place the pellet in the vessel. Add 10 mL of a 2% soluble starch solution. The copper causes a green colour inside the cell, and as the cell generates iodine it reacts with the starch to form a blue-violet colour within a few minutes. The simplest description of the reactions that are occurring is as follows :
• Cu2+ + I- => Cu+ + 1/2I2
• Cu+ + H2O2 => Cu2+ + OH. + OH-
• OH. + I- => OH- + 1/2I2
A fungus-like, soft membrane grows out of the mixture, enclosing a hollow cavity up to 1 cm across. Chemicals diffuse through this membrane, react inside the cavity, and then diffuse out, creating swirling clouds of violet liquid in the green base solution. Rather than reaching equilibrium, this process persists : the reactions are reminiscent of the way living cells sustain themselves, driven from equilibrium by the flow of chemicals and energy across their membranes. Sometimes the cell structures grew into forms with several lobes, or sprouted buds that split off from the parent membraneref.
• extinct organisms (palaeobiology) : there have been 5 extinctions since the birth of multicellular life 600 million years ago. In each, 65-95% of the world's species died out (see also extinction endangered species
  
  )
• the Permian-Triassic extinction was the most extreme in Earth's history. It has been difficult in part to determine the environmental conditions that may have led to the extinction. A detailed chemical analysis of marine sections obtained by drilling off western Australia and South China suggests that the upper part of the oceans at the time of the extinction were extremely oxygen poor and sulfide richref. In contrast, other reconstruct a record of the terrestrial vertebrate extinctions in the Karoo Basin, Africa. This area preserves the most detailed vertebrate fossil record from this time, but correlating rocks in different parts of the Basin has been problematic. Using paleomagnetism and carbon isotopes, they show that extinctions were accelerated up to a pulse at the boundary, and that the pattern of appearance of Triassic fauna may imply that some originated even before the final pulseref.
• Australia's earliest settlers drove many animals to extinction through their use of fire. Many large Australian animals are known to have died off after man first arrived on the continent around 50,000 years ago. But it has remained unclear exactly how, if at all, humanity caused this extinction. Some experts have argued that early settlers unleashed a 'blitzkrieg' of hunting on the animals, wiping them out in a matter of generations. Others have argued that the aboriginals brought novel diseases with them from overseas. Neither of those is the real story : humans' extensive use of fire altered the makeup of plant ecosystems, leading to a widespread die-off of creatures that fed on certain grasses. Many animals changed their eating habits soon after humanity's arrival, and that those that were unable to adapt to new foods died out. The researchers studied preserved eggshell fragments from Lake Eyre, Port Augusta and the Darling-Murray Lakes in southern Australia. Some of the eggs came from the emu (Dromaius novaehollandiae), which survives as a species today; others belonged to the similar, but extinct bird Genyornis newtoni. Miller's team reconstructed the birds' diets over the past 140,000 years by studying the levels of radioactive carbon isotopes in the eggshells. They found that Dromaius shifted from nutritious grasses, which the team identified by its distinctive levels of radioactive carbon, to less nutritious shrubs and trees around 45,000 years ago. A similar trend was seen in wombat teeth. But Genyornis showed much less variation in its diet, which may explain why it failed to adapt and survive into the present. The change in diet is down to man's extensive burning of grasslands, to clear passageways, open up hunting grounds or signal over long distances. The enterprise of the first colonists altered ecosystems at their lowest level: the vegetation, and as vegetation changed, those animals with flexible dietary tolerances were able to adjust to the changed food sources, whereas those with more specialized dietary needs became extinct. No climate shift is known to have occurred in Australia during the time of that extinction. So they argue that humanity, rather than climate, caused a change in vegetation, and widespread extinctions. Others are not so sure. Fossils found at Cuddie Springs, New South Wales, seem to indicate that ancient fauna lived side-by-side with humans for several thousand years before finally succumbing to encroaching desertification as little as 30,000 years ago. But more accurately dated fossils are needed to support this theory. The Cuddie Springs dating remains very contentious : most agree that the extinction event occurred between 50,000 and 45,000 years agoref
• dinosaurs : they extincted about 65 million years ago at the Cretaceous-Tertiary (KT) transition. According to conventional paleontological wisdom, an asteroid or comet 10 to 14 kilometers wide crashed into the present-day Yucatán Peninsula and wiped out the dinosaurs. Most scientists currently consider the Chicxulub impact crater, perhaps about 145 km wide, to be the smoking gun of this extinction, but actually the collision that created the Chicxulub crater happened before the KT extinction--300,000 years too soon, to be more precise. Dinosaurs may have been forced into extinction partly because there were too few females. The creatures died out roughly 65 million years ago, around the time that a huge meteor slammed into earth. Some scientists believe that the immense dust cloud thrown up caused swings in the climate that the dinosaurs were unable to survive. However, it is not clear exactly how the temperature change killed them off. If dinosaurs used temperature to determine the sex of their offspring, climate changes could have messed up the ratio of males to females. This idea is based on the reproduction of modern day reptiles such as crocodiles, to which dinosaurs are related. Crocodiles' sex depends on the temperature at which their eggs are incubated. Male crocs hatch in moderate temperatures, while females emerge if the heat rises or falls by a few degrees. In the case of dinosaurs, that changes in temperature after the meteor impact favoured the birth of males. Over time females would become rare, causing fewer young dinosaurs to be born and species to dwindle to extinction. Palaeontologists currently believe that dinosaurs started dying out around 10 million years before the meteor impact. This was accelerated by a swathe of volcanic explosions and sea level changes that upset the climate, although the details remain unknown. If the sex ratio was skewed to 80:20, for example, the model shows that a population of 1000 animals would die out within 50 rounds of reproduction. That might represent only 500-1000 years, depending on the animal's fertile lifespan. The majority of dinosaur experts believe that the animals are most closely related to birds, which do not use temperature to determine sex. Either way, it is hard to confirm: we do not have Triceratops or Tyrannosaurus rex eggs to incubate. Miller's analysis also has to explain why some animal groups that use temperature to determine sex survived the change in climate. Crocodiles, for example, lived through the same climate shift. They may have been able to protect their eggs from temperature extremes because they lived near cooling streams, or were able to adapt to the changing conditions faster than the long-lived dinosaurs. Other more robust ways of determining sex might have evolved partly because temperature-dependent sex determination is so risky. Today, most animals including humans use genes to determine sex, so that males inherit one set of sex chromosomes and females another. This ensures a stable sex ratio regardless of meteors or extreme weather. Some reptiles have clung to the more primitive mechanism. This could be because they live in climates in which their eggs are protected from large swings in temperature. But that leaves these species, which include long-lived turtles, vulnerable to future climate change from global warmingref
• roughly 230 million years ago, the creature Dinocephalosaurus orientalis swam in shallow seas off the coast of Pangaea, the supercontinent that dominated the Earth at that time. Some mishap entombed one of them in limestone near Xinmin, Guizhou Province, in southern China. Its neck, which is almost twice as long as its reptilian body, supported a relatively tiny head complete with a nasty set of fangs. But the specimen's most surprising characteristic is that, just as we have ribs protruding from the vertebrae in our backs, this creature has little riblets emerging from its 25 or so neck vertebrae. These are long and overlapping, and ran parallel to the beast's spine, so they would have stiffened the neck considerably. Prehistoric aquatic animals with extravagantly long necks were, until now, thought to use their necks like snakes, lunging and twisting as they raced after prey, or like periscopes, to breathe at the surface. If you found such an animal that lived in the water, you'd say it had a long snaky neck. But Dinocephalosaurus could not have used its neck in such a way. Its throat was too long to properly inflate the lungs if used periscope-style, because the pressure difference between the surface and the depth of the lungs would have been too great. What is more, Dinocephalosaurus had more vertebrae and longer neck ribs than its ancestors, indicating that the stiffness may have conferred some advantage and been selected for over time. The creature's head and teeth gave LaBarbera a clue to what the neck might have been used for. They seem to be set up for suction feeding. This is a common tactic of aquatic predators in which prey is sucked into the gullet by a dramatic expansion in the volume of the mouth. Some think that Dinocephalosaurus used a variation on the suction tactic. Instead of expanding the mouth, the muscles attached to the neck ribs could have pulled them outwards, expanding the volume of the throat. Because of the neck's length, this manoeuvre would produce plenty of suction. The neck is a long cylinder, and if you increase the diameter a little bit you increase the volume significantly. You suck in, and you secure the prey between the teeth. This then keeps the mouth open while you push the water out of your neck. And then comes the swallowing. Other possible uses for a stiff neck include faster swimming and stealth camouflage. In murky water, the innocent prey would see only the unassuming head of the beast and not its large body, far away in the gloom.
• pterosaur flying reptiles were contemporaries of the dinosaurs and abounded in the Early Cretaceous period when the fossil was created, around 121 million years ago. A fossil including imprints of wing and skin tissue as well as bones and shell was found at Jingangshan in the Liaoning province of northeastern China and confirms the long-standing theory that the creatures laid eggs rather than giving birth to live young : a natural disaster such as a volcanic eruption dealt it a swift death and caused the egg to be delicately preserved. Its well-developed shoulder and chest bones, and elongated fourth finger, mark it out as a pterosaur. At just 53 millimetres long and 41 millimetres wide, it is slightly smaller than a typical hen's egg. But the embryo boasts a 27-centimetre wingspan that would have more than quadrupled by adulthood. What's more, the well developed wings suggest that it would have been able to fly and feed independently of its parents soon after it hatchedref.




A remarkable specimen has been discovered of an Early Cretaceous pterosaur that has a tooth embedded in one of its cervical vertebrae: the tooth has been identified as one from a spinosaurid theropod dinosaur. This fossil is direct evidence that spinosaurs included items other than fish in their dietref.
• Psittacosaurus : in Liaoning, China a fully grown individual has been found surrounded by 34 youngsters, all huddled within an area of 0.5 square metres. It is almost certainly a family group rather than a happenstance collection of dead dinosaurs. Although some groups of dinosaurs, such as theropods and hadrosaurs, are thought to have made nests, the find seems to be the first clear example of dinosaur parenting. It is not clear whether the 75-cm-long adult is a male or a female, but the doting parent's sex was not necessarily of any consequence when it came to looking after the kids. In many living bird species, both parents help out in the nest. The youngsters are all around 20-centimetres long, suggesting that they represent a single brood. Although a volcanic eruption might seem the obvious culprit, Varricchio says that it is hard to imagine volcanic ash burying the dinosaurs quickly enough to preserve them like this. It is more probable, he suggests, that they were entombed when an underground burrow collapsed, or drowned by rising flood waters. Many of the dinosaurs have their heads raised, which might indicate such an event. Barrett adds that the bowl-like depression in which the fossils were found is reminiscent of a nest, although he adds that this is very speculative. Earlier findings have hinted at the possibility that psittacosaurs might have lived in groups containing three or four adults, meaning the single-parent family may not have been the normref.
• Tyrannosaurus rex, which roamed the earth some 65 million years ago, was one of the largest terrestrial carnivores ever to live. Adults typically weighed in at around 5,000 kilograms, making them at least 15 times larger than today's largest land-based meat-eater, the polar bear. Some experts believed they grew slowly throughout their lives, like modern-day reptiles. Others thought they had an initial growth spurt that later subsided, like that in birds and mammals.  It gained up to 2 kilograms a day, as much as a modern-day African elephant does. But assessing growth rates is tricky, as the creatures are difficult to age. The standard method for using a fossilized skeleton to estimate the age at which a dinosaur died is to count growth rings. These are dense mineral deposits that are laid down in the bones on a yearly basis, as the animal grows. But the technique generally looks at large, weight-bearing bones such as the thigh. In therapods, such as T. rex, these bones are hollow, so the vital rings are missing. Instead the team looked at bones that do not bear weight, such as ribs and shinbones, which are solid in T. rex. The researchers tested the method in alligators and lizards of known ages and found that they were able to accurately predict what their lifespans had been. The researchers then turned their attention to 7 T. rex fossils of varying sizes. Using the new method, the team found that the specimens were likely to be between 2 and 28 years old when they died. This made Sue, the oldest and best-preserved T. rex, 70 years younger than was previously thought. By combining the dinosaurs' ages and sizes, the researchers worked out their growth rates. T. rex, it seems, grew up fast. The animal grew most between 14 and 18 years of age, then retained its large size throughout the rest of its life. Like T. rex, the growth spurt of 3 smaller tyrannosaur species that existed before occurred over a 4-year stretch, but their rate of growth was around 4 times slower. This suggests that T. rex evolved to be so big because of its exceedingly fast growth rate. As it got bigger, T. rex probably suffered from a progressive decline in its running ability. Younger, smaller animals could have reached speeds of up to 40 kilometres per hour. But as their weight passed 1,000 kilograms, just a fifth of the adult size, this would have become biomechanically impossible. For those who believe T. rex was a hunter rather than a scavenger, it is a mystery how the animals managed to eat enough to maintain their growth spurt, given that their ability to chase prey would have been seriously impairedref. Ancestors of T. rex were clothed in delicate feathers, a 130 million-year-old fossil discovered in China suggests. The find may come as a surprise to people used to images of Tyrannosaurus as a scaly monster. But many palaeontologists have been predicting just such a find ever since the first evidence of a dinosaur with a feathery coat came from the same site : the new dinosaur has been christened Dilong paradoxus. Dilong means Emperor dragon, while paradoxus as it is counter-intuitive to think of feathers and a Tyrannosaurus together. Evidence of these so-called protofeathers is usually difficult to find because feathers decay when they are exposed to oxygen. But at Liaoning, the specimens appear to have been buried extremely quickly under fine-grained volcanic ash, helping to preserve the soft, feathery outlines. Feathers evolved on dinosaurs long before the appearance of birds. Until now, some palaeontologists have been dubious that feathered tyrannosauroids existed. The jackal-sized Dilong was far smaller than T. rex, but Dilong shares many of its characteristics. The meateater probably had a broad, square skull and powerful jaws. But while the forelimbs of T. rex had dwindled until they were almost useless, Dilong would have been able to clutch food in its hands and bring it to its mouth. Dilong's protofeathers are not what we would recognise as feathers today, but are their evolutionary precursors. Rather than having a central shaft and barbs, they are single flexible filaments that would have covered the dinosaur's body like hair. The protofeathers would most likely have been used for insulation rather than flight. The giant T. rex had probably lost the featherlike features of its predecessors because, with its much larger size, it would have had more difficulty losing heat than keeping it. Tyrannosaurus chicks may have had a downy cover, though. A thigh bone from a 70-million-year-old Tyrannosaurus rex has given fossil experts an unexpected treasure: well-preserved soft tissue. The stretchy material, which may contain the remnants of blood vessels and cells, could shed light on how dinosaurs' bodies worked. Although palaeontologists have had plenty of bones with which to work, they have struggled to find relics of the muscles, organs and blood vessels that once kept giants like T. rex on the move. These soft tissues decay quickly and are rarely fossilized. So far, the best view inside dinosaurs has come from rocky fossils that preserve the shape of the original tissue. Even these finds are extremely rare, as they are only produced when minerals replace these soft parts or fill in the cavities they leave after decaying. Now, however, researchers have got their hands on the real thing. The fossil was unearthed in Montana : most palaeontologists don't look inside bones, in fact, they do their best to keep them intact. But Schweitzer and her colleague Jack Horner, of the Museum of the Rockies in Bozeman, Montana, prefer to think of them as 'wrapping paper' for the once-living material inside. To isolate the soft tissue lining the bone's marrow cavity, they co-opted a technique used to study modern bone : the hard, calcium-containing component dissolves, leaving a supple matrix behind. From this matrix, the treatment released translucent vessels that floated freely in solution. They were spotted with small, red-brown dots that may be nuclei of the cells that formed the vessel. Inside the vessels, the researchers found tiny structures that look like osteocytes. Surprisingly, they resembled cells from modern ostrich bone, right down to details such as the oval shape of the putative nuclei, and flexible extensions from the cell membrane that are used to exchange waste. Although the seeming cells and blood vessels are organic, the researchers don't know whether they represent the original material or a new type of fossilization that has not been seen before. If they could sequence actual protein fragments from the sample, the researchers could learn much more about how dinosaurs are related to modern animals, especially birds. They might even find out whether T. rex was warm- or cold-blooded. Tissues from other ancient organisms, such as insects trapped in amber, have been discovered almost intact. But Schweitzer and her colleagues still don't know how this dinosaur tissue has remained so well preserved for so long. It is possible that other ancient vertebrate fossils could contain soft tissue, potentially paving the way for comparisons between species : this sort of information becomes a lot more significant if there's a chance of finding it for a range of different types of dinosaurs and fossil vertebrates. Schweitzer is reluctant to say whether she is attempting to isolate DNA from the tissue. But could such work lead to the recreation of dinosaurs, in the style of the Hollywood blockbuster Jurassic Park? DNA cannot survive that long.
• Competing for food in the wild can be a pain in the neck, so a dinosaur known as Brachytrachelopan mesai evolved a shorter one. A fossil has recently been discovered of this short-necked dinosaur that lived in Patagonia, Argentina, about 150 million years ago, during the Late Jurassic period. It is a member of the sauropodgroup of dinosaurs, which includes the 30-metre-long giant Diplodocus. Sauropods typically had long necks, which is thought to have allowed them to reach high into trees to maximize their food intake. But the fossil of B. mesai shows that it measured less than 10 metres, even after reaching adulthood. A long neck is an unnecessary and energetically expensive asset for a creature if food is readily available on the ground, and this could explain the existence of B. mesai. Nature tends to eliminate structures that are not needed for that reasonref. It was a really well-preserved specimen, although we found it a few thousand years too late after erosion had already begun to have an impact. Patagonia lacked bird-footed dinosaurs called ornithopods, which grazed the Jurassic plains of other continents. This means that B. mesai might have faced little competition for resources. This particular fossil also provides exciting clues about the evolution of sauropods. The short-necked dinosaur's closest relative comes from Africa. Brachytrachelopan mesai bears less similarity to more recently evolved sauropods in South America, and even weaker resemblance to those in Northern continents. All of this hints that it evolved swiftly in the middle Jurassic period, after the separation of continents of the Southern and Northern Hemispheres but before Africa and South America fully broke apart. It looks like this is a dinosaur that's trying to reinvent itself : this fossil is telling us a lot about how these ecosystems evolved.
• Archaeopteryx, the earliest known flying bird (avialan) from the Late Jurassic period, soared above the still lagoons of Bavaria 147 million years ago : the first fossilized remains were found in 1861. The recognized finds all hail from a 25-square-kilometre patch of quarry in Bavaria, Germany, known as the Solnhofen Limestone. Over a million years ago, the area boasted a series of stagnant lagoons lined with thick silt. The birds either lived in the area or were passing through when they fell in. The oxygen-poor waters would have slowed their decay, allowing their feathers and bones to leave intricate impressions in the fine silt. The enigma combines the feathered wings and wishbone of birds with the teeth and long, bony tail characteristic of reptiles, causing many to view it as an intermediate between the two groups. It exhibits many shared primitive characters with more basal coelurosaurian dinosaurs (the clade including all theropods more bird-like than Allosaurus), such as teeth, a long bony tail and pinnate feathers. However, Archaeopteryx possessed asymmetrical flight feathers on its wings and tail, together with a wing feather arrangement shared with modern birds. Archaeopteryx closely resembled modern birds in the dominance of the sense of vision and in the possession of expanded auditory and spatial sensory perception in the ear. Archaeopteryx had acquired the derived neurological and structural adaptations necessary for flight. An enlarged forebrain suggests that it had also developed enhanced somatosensory integration with these special senses demanded by a lifestyle involving flying abilityref
• discovering evidence of behaviour in fossilized vertebrates is rare. Even rarer is evidence of behaviour in non-avialan dinosaurs that directly relates to stereotypical behaviour seen in extant birds (avians) and not previously predicted in non-avialan dinosaurs. A new troodontid taxon was discovered from the Early Cretaceous Yixian Formation of western Liaoning, China. Numerous other 3D preserved vertebrate fossils have been recovered recently at this locality, including some specimens preserving behavioural information. The new troodontid preserves several features that have been implicated in avialan origins. Notably, the specimen is preserved in the stereotypical sleeping or resting posture found in extant Aves, showing that this position might have evolved before they did. Evidence of this behaviour outside of the crown group Aves further demonstrates that many bird features occurred early in dinosaurian evolution. The dinosaur, named Mei long, or 'soundly sleeping dragon', has lain undisturbed for almost 140 million years. M. long seems to have died with its hindlimbs folded underneath it and its head tucked under one forelimb, just as birds roost with their head under their wing. It is the oldest known fossil found in this postureref
• sauropterygians lived throughout the Mesozoic era, from 250 to 65 million years ago : since the first description of a plesiosaur in 1821, thousands of related sauropterygian marine reptile specimens have been collected, but no direct evidence has been found to determine whether they came on shore to lay eggs (oviparity) like sea turtles, or gave birth in the water to live young (viviparity) like the ichthyosaurs and mosasauroids (marine lizards). Many contended that the reptiles laid their eggs on the shores�as modern marine turtles do, but in 2004 the evidence of viviparity came in the form of 2 small, nearly complete, gravid specimens of the sauropterygians Keichousaurus hui from the province of Guizhou in Middle Triassic (200-million-year-old) sediments in southwestern China. Most of the embryos found within the nearly 12-inch long females were "head backwards," a position thought to be abnormal, which the authors suspect could have caused the death of the 2 mothers and their young. These 2 specimens speak very nicely, very neatly, and very cleanly of the fact that the ability to give birth to live young arose very early on in the evolution of these groups of reptiles. They provide clear evidence of sexual dimorphism in sauropterygians, and indicate that plesiosaurs and their close relatives did give birth to live young. The findings also answer questions about more evolved groups of sauropterygians, such as the giant plesiosaurs. Giving birth in the water would have been advantageous, since animals thus avoid the risks associated with going on land to reproduce. One interesting anatomical feature of the Keichousaurus specimens is the presence of a very loose attachment between the pelvic girdle and the sacrum, in contrast with the more solid connection found in land animals. That loose type of joint has been interpreted as an adaptation to aquatic environments, allowing movement and thus reducing physical stress during sudden stops or turns in the water. The chain-like connection present between the pelvis and the sacrum would also have allowed the pelvic girdle to change its shape, maximizing the space of the birth canal. The discovery of viviparity in the Keichousaurus hui fossils also enabled determination of the gender of the existing morphotypes�particular specimens that define the characteristics of the group�of this dimorphic species, known until now as "sex X" and "sex Y." The specimens, unequivocally female, led the authors to the identification of sex X as the female and sex Y as the male, based on the structural complexity of the humerus and on the length ratio between the humerus and the femurref.
• mesozoic mammals are commonly portrayed as shrew- or rat-sized animals that were mainly insectivorous, probably nocturnal and lived in the shadow of dinosaurs. The largest known Mesozoic mammal represented by substantially complete remains is Repenomamus robustus, a triconodont mammal from the Lower Cretaceous of Liaoning, China. An adult individual of R. robustus was the size of a Virginia opossum. A new species of the genus has been reported, represented by a skeleton with most of the skull and postcranium preserved in articulation. The new species is 50% larger than R. robustus in skull length. In addition, stomach contents associated with a skeleton of R. robustus reveal remains of a juvenile Psittacosaurus, a ceratopsian dinosaur. These discoveries constitute the first direct evidence that some triconodont mammals were carnivorous and fed on small vertebrates, including young dinosaurs, and also show that Mesozoic mammals had a much greater range of body sizes than previously known. Mesozoic mammals occupied diverse niches and that some large mammals probably competed with dinosaurs for food and territoryref. Repenomamus giganticus was > 1 metre long, about the size of a large dog and large enough to feast on young dinosaurs, exploding the myth that all of the mammals living back then were relatively tiny. The fossil, which dates back 130 million years, has a skull that is double the size of that of R. robustus. This makes it a startling addition to the ranks of Mesozoic mammals, who lived with the dinosaurs > 65 million years ago. If R. robustus could manage to eat a dinosaur, then its big brother almost certainly could : however, it may well have fed on plants and insects too. Anyway with these teeth you wouldn't expect them to do a lot of grinding or crushing, and that's what you would need, like a pestle and mortar. The dinosaur bones found with R. robustus are from a single individual and some are still articulated, making it unlikely that they were washed there from elsewhere after death. The bones' articulation also suggests that Repenomamus tore its prey limb from limb before gulping it down in large chunks. This theory is bolstered by the fact that the mammals' teeth are sharp, with no molars. One way to confirm that the Psittacosaurus was eaten would be to look for corrosion on its bones from digestive acids : mammalian carnivores today have very strong digestive juices. Hyenas' stomach acid, for example, can make holes in bones and teeth
• fossil-hunters working in the dusty Utah desert have caught a dinosaur in the act of going vegetarian. The newly discovered species, which lived about 130 million years ago, displays the hallmarks of adapting to a leafy diet. The species, christened Falcarius utahensis, belongs to a dinosaur group called the therizinosauroids. These are mostly thought to have been plant eaters. But the recently discovered fossil, the most primitive therizinosauroid found so far, seems to have survived on a mixed diet of meat and veg. Researchers uncovered a skull, pelvis and limb bones belonging to the species at Cedar Mountain in eastern Utah. From the fossils they conclude that F. utahensis walked upright, standing more than a metre high and measuring some 4 metres from tip to tail. The creature's teeth have a shape that seems to be adapted to leaf shredding, the researchers report. Similar teeth can be found in modern iguanas, for example, a reptilian family that also has a varied diet. Falcarius utahensis also has a slightly widened pelvis, which would have been necessary to accommodate the longer gut needed to extract nutrients from plants. But the dinosaur's legs reveal that it still has adaptations suited for meat eating as well. The creature's thigh bones were longer than its shin bones, suggesting that it could run at an impressive pace. The legs are still adapted for running after prey. Later therizinosauroids have longer shin bones, which suggests that they waddled around like long-legged birds. The switch to vegetarianism is surprising. The therizinosauroids belong to a larger group of dinosaurs known as theropods, and many of these are known to have been excellent at catching a meaty meal. Nobody understands why theropods should revert to herbivory when they're such excellent predators. Perhaps certain dinosaurs were pushed along the evolutionary route to vegetarianism because they lived in an area where there was no other plant-eating competitor. Falcarius utahensis's diet is not its only noteworthy feature; its North American home is also a surprise. Until now, therizinosauroids have been found almost exclusively in China, which led experts to believe the group arose there. This was considered a nearly pure Asian group. Finding the most primitive member of the group in Utah throws that into question. The team now suspects that therizinosauroids once roamed over most of the Northern Hemisphere.


• dinosaurs' hollow bones may have given them the puff to lead active lifestyles. A fossil find shows that the group of dinosaurs that included Velociraptor and Tyrannosaurus rex probably used the same super-efficient respiratory system that birds have today. The fossil, which is of a carnivorous dinosaur called Majungatholus atopus, shows that its bones included spaces for storing air. This would have allowed the species to have the quick metabolism necessary for an active predatory lifestyle. Birds have fast metabolic rates thanks to their efficient way of extracting oxygen from the air. They have two lungs, as mammals do, but the airflow through them is controlled by a complex system of air sacs throughout the body. Most birds have 9 such sacs, which also extend through their hollow bones. The structure of air sacs in M. atopus's vertebrae were compared to those in > 200 living birds. The structures were very similarref. This study paints a clearer picture of how these organisms would have existed in their environment. It indicates that these animals had the potential for a high metabolic rate. Birds are thought to be direct descendants of theropod dinosaurs, the group to which M. atopus belongs. Palaeontologists already have evidence that the extinct creatures were similar to their descendants, with high growth rates, bird-like sleeping postures and even feathers. This study forms part of an increasingly robust story that says birds are essentially dinosaurs, but smaller. Using functional work in live animals is a nice addition, and perhaps now you could go as far as saying dinosaurs had a bird-like metabolism. The efficient breathing system of birds is older than previously thought, but it seems that a breathing system like this is of more ancient origin, from nearer the base of the dinosaur family tree. Finding older dinosaur fossils would support this, and perhaps show that other bird-like characteristics are older than suspected. Some palaeontologists still dispute that dinosaurs were closely related to birds, and have suggested that their breathing systems were more like those of crocodiles. This work is another nail in the coffin for that competing theory
Web resources :
• Museum of Paleontology
• The Field Museum
• The Natural History Museum
• American Museum of Natural History
• dodo (Raphus cucullatus) of Mauritius may have persisted until 1690, some 28 years beyond its accepted extinction date of 1662.
• Tasmanian tiger (Thylacinus cynocephalus)
• mammoth : you might call them the Marilyn Monroes of the mammoth world. An analysis of 43,000-year-old DNA from these prehistoric creatures suggests that some of them were blondes. Textbook pictures of woolly mammoths (Mammuthus primigenius) typically depict the shaggy beasts sporting a coat of brown hair. But they probably came in a range that also featured lighter browns and auburns. Some naturalists already suspected that a few mammoths might have been blonde. Hairs found buried in the frozen tundra, where the creatures lived until their extinction some 3,500 years ago, come in range of different shades. But we didn't know if it was genetic or just a result of being in the ground for tens of thousands of years. Rather than studying the hair itself, he and his colleagues turned to ancient mammoth bone to solve the conundrum. They took samples from a 43,000-year-old bone found in Siberia, and extracted the portion of DNA containing a key pigmentation gene, Mc1r. Most mammalian genes are present in two copies - one from each parent. Hofreiter and his team found that this mammoth's two copies of Mc1r differed slightly. And when they investigated the proteins produced by the 2 versions, they discovered that one functions far better than the other in producing brown pigmentref. The more effective version of the gene is responsible for richly pigmented brown hair, the researchers suggest. The weaker version probably produces lighter brown, blonde or reddish shades. The researchers knew which gene to look for because all mammals possess versions of the Mc1r gene. A single copy of the strongly acting version is enough to create brown hair, which is why natural blondes are in the minority in humans; ordinarily it takes two copies of the weaker version to give lighter shades. Mutations in the gene are associated with lack of pigment; rare blond versions versions of the American black bear can attribute their distinctive looks to defects in the same gene. With one copy of each version, the 43,000-year-old mammoth in this study was probably a brunette. Samples from three more mammoths also failed to find one that would have been blonde. But the fact that the 'blonde gene' was present in the population gives credence to the theory that light-coloured hairs found in the ice genuinely reflect their owners' coat colours. It is impossible to say, without unearthing a fully preserved mammoth, whether they would have been uniform in colour or whether patterns of different hair colours mdash; from spots to stripes mdash; were possible. It is also unclear whether blonde or brown mammoths would have enjoyed a natural advantage, although it seems unlikely given that they had little need for camouflage. More important, was the thickness of the mammoth's hairy coat in protecting against the icy tundra weather. It would maybe have been icy and snowy, and certainly very cold
Web resources : Extinct organisms that are represented with sequence data at GenBank at NCBI Taxonomy Browser

• Taxonomy Browser at NCBI contains only those organisms that are represented in the genetic databases with at least one protein or nucleotid sequence. The browser shows by default 3 levels of the classification hierarchy. The little circles or squares that precede the name of each taxon in the indented list do not carry any biological information. In particular, they show only taxonomy tree-related information. Square before taxon name means that it is leaf element of taxonomy tree. Circle means that taxon has children in taxonomy tree. If circle was not filled then taxon children are shown. If circle is filled it will mean that taxons' children exist but not shown on the current page. In this case You need to click on the taxon to see its children.
• dmoz Open Directory Project (ODP) : Taxonomy
• Phylogenetic classification and the universal tree
• Integrated Taxonomic Information System (ITIS)
• Understanding Evolution at University of Berkeley
• Biodiversity and Biological Collections Web Server
• Discover Life by the Polistes Foundation
• European Register of Marine Species
• Hawaian flora and fauna checklists
• Index of Organism Names
• Back to top
• Species 2000
• Talk Origins
• Tree of Life web project
• International Commission on Zoological Nomenclature (ICZN), based at the Natural History Museum, is called ZooBank.
• uBio Taxonomic Name Server
• Species 2000
• Wikispecies
• GenBank
• Barcode of Life
• Phylogenetics resources at Museum of Paleonthology at Berkeley
• Paleontology :
• dmoz Open Directory Project (ODP) : Paleontology
• Paleomap Project by Christopher Scotese
• Paleo Ring
• University of California Museum of Paleontology (UCMP)
• Usenet sci.bio.paleontology
• Anthropology
  
• What are orthologous and what paralogous genes ?
• Nucleomorphs
• Conjugation between bacteria and mammalian cells
• Usenet
• bionet.organisms
• sci.bio.systematics

• there could be as many as 10 million or even 100 million animal species. Biologists have described about 1 million so far - each new animal requires a lot of time and expertise. Not only is the number of described species a very small proportion of the estimated extant number of taxa, but it also appears that all concepts of the extent and boundaries of 'species' fail in many cases. Using conserved molecular sequences it is possible to define and diagnose molecular operational taxonomic units (MOTU) that have a similar extent to traditional 'species'. Use of a MOTU system not only allows the rapid and effective identification of most taxa, including those not encountered before, but also allows investigation of the evolution of patterns of diversity. A MOTU approach is not without problems, particularly in the area of deciding what level of molecular difference defines a biologically relevant taxon, but has many benefits. Molecular data are extremely well suited to re-analysis and meta-analysis, and data from multiple independent studies can be readily collated and investigated by using new parameters and assumptions. Previous molecular taxonomic efforts have focused narrowly. Advances in high-throughput sequencing methodologies, however, place the idea of a universal, multi-locus molecular barcoding system in the realm of the possibleref. DNA barcodes�a 648-bp region of the mitochondrial gene cytochrome c oxidase I (COI)�are either identical or very similar within species, but differ between species. Mitochondria - cellular powerhouses with their own genomes - are good for genetic identification because there are many copies in each cell, and their DNA evolves relatively quickly, creating differences between species. Single gene reads will deliver an unambiguous species identification in more than 95% of animal cases within a decade. Very young species might prove the stumbling block, though, for which additional sequences might be informative. A practical difficulty with the approach is to capture molecular geographic variation within each species. This is especially important for low-dispersal or geographically structured taxa, which probably include the majority of the world's species. Birds tend to be vagile creatures, and therefore less likely�all else being equal�to show substantial geographic variation than more sedentary species, such as snails or small mammals. It will complement rather than replace a 250-year tradition of Linnean taxonomy. Linnaeus, to give his familiar, Latinised name, introduced the system of binomial nomenclature in 1758 by classifying > 10,000 species of animals and plants with 2-part names, also Latinised. Around 1.5 million species are thought to have been described so far, but > 6 million names have been used. Most taxonomists agree with the basic principle of ZooBank. There are, however, disagreements about exactly how it should work. 2 of the least tractable are who gets to decide which names are chosen, if there is a dispute�and which names are unacceptable in any circumstances. At the moment, the validity of a name depends on precedent, which has led to the unwelcome re-dubbing of familiar species on the basis of long-forgotten specimens that have come to light in the dusty corners of collections. One notorious example was the translation of a familiar dinosaur, Brontosaurus, into Apatosaurus. A more important case is Aedes aegypti, the mosquito that transmits yellow fever and dengue, which, to the horror and confusion of medical entomologists, was renamed Stegomyia aegypti on what many consider flimsy evidence. What name a genuinely new species is given, though, is entirely up to the discoverer. Hence the existence of Anophthalmus hitleri, a blind cave beetle named in 1933 after Adolf Hitler. In this context, the recent naming of another beetle after the American president is hardly a hanging offence, although Mr Bush may not be flattered by the company. But when the scientific underpinning of taxonomy itself is threatened by politics, different questions arise. Last year, for example, there was a nasty row in Turkey between Kurdish and Turkish taxonomists over whose names should apply to some local animals. The Kurds accused the Turks of renaming several species to remove any trace of Kurdishness. Another issue is the sale of animal names. This is not yet commonplace, but an interesting precedent was set last year when a Canadian gambling company bought the right to name a newly discovered species of South American monkey. Here, ZooBank could help by providing some sort of guarantee that such a precious asset will not vanish in a puff of nomenclatural smoke. Whilst studies using the COI sequence are an excellent place to start, the rapidly advancing pace of molecular techniques makes it hard to predict what methods will be used in 20 or even 10 years' time
• number of species of living organisms in the World : 13.6 million
• Insects : 8,000,000
• Fungi : 1,500,000
• Bacteria : 1,000,000
• Arachnids : 750,000
• Viruses : 400,000
• Algae : 400,000
• Nematodes : 400,000
• vascular plants : 320,000
• Protists : 200,000
• Molluscs : 200,000
• Crustaceans : 150,000
• Vertebrates : 50,000
• other total : 250,000
< 20% of the Earth's estimated 10 million species of plants and animals have been named. Researchers working on the Barcode of Life Initiative hope that genetically identifying all of them in a standardized way on a global scale will speed up the discovery of new ones. The initiative will begin with 3 projects : one will provide barcodes for the 10,000 known species of birds by 2010, another will tackle the 23,000 types of marine and fresh water fish and a third will genetically label the 8,000 kinds of plants in Costa Rica, Central America.
Web resources :
• Consortium for the Barcode of Life (CBOL)
• International Conference for the Barcoding of Life
• the principles of face recognition software are being used to identify individual whales or dolphins from photos of their fins or flippers, making easier for researchers and conservationists to track marine mammals for understanding the behaviour of marine mammals and evaluating the status of different species in the wild, without the need for physical brands or tags. In the past, biologists have tagged animals such as whales using branding with heat or liquid nitrogen. But as well as being rather impractical, it is not clear whether such approaches harm the animals or affect their behaviour. Chandan Gope at the University of Texas, Dallas, and his colleagues have developed software that analyses the pattern of curves at the edges of dolphin dorsal fins, whale flukes or sea-lion flippers. The shapes of these body parts change little over time, so they provide a reliable 'fingerprint' that can be spotted in different photos of the same animal. The computer program works by picking out the distinguishing points along one of these edges and then digitally recreating the contour. It then compares the curve with others from a database and highlights the best potential matches. Previous studies have tried to use these curves to recognize specific individuals, but they have had problems comparing pictures taken from different angles. The software overcomes this challenge by using a trick known as an "affine transformation". This mathematical method allows you to rotate a line while preserving the relationships between its points, including the ratio of distances between them. This improved method of matching photos will enable marine biologists to identify individual animals faster. The program narrows down the number of options, producing a shortlist from which the user can make a final match by eye. Half of the time the user found a match within the first seven images suggested by the computerref

Web resources : The Marine Mammal Center
• the sea, covering 70% of the Earth's surface, offers a considerably broader spectrum of biological diversity than terra firma, containing approximately 75% of all living organisms
• the oceans contain 3 x 1028 bacteria

• Ax, P. 1987. The phylogenetic system. The systematization of organisms on the basis of their phylogenesis. John Wiley and Sons, Chichester.
• Jeffrey, Charles 1977. Biological Nomenclature 2ed. Edward Arnold Publishers Limited.
• Minelli, A. 1993. Biological systematics. The state of the art. Chapman & Hall , London.
• De Queiroz, K. & Gauthier, J. 1992. Phylogenetic taxonomy. Ann. Rev. Ecol. Sy st. 23, 449-480.

About this site  |  Site map  |  Acknowledgements |  Current link partners
 Abbreviations and acronyms  |  Medical terminology  |  Add a link  |  Translate   |  Softwares | 

Cite this page!

---

---

What is arrangement of organisms into groups taxa on the basis of similarities or relationships?

What is the arrangement of organisms into taxonomic groups known as taxa )?

What is the system of arranging organisms into groups based on relationships between different organisms?

What is the arrangement of organisms called?