Phylogenetics
In biology, phylogenetics is the study of the evolutionary history and relationships among individuals or groups of organisms. These relationships are discovered through phylogenetic inference methods that evaluate observed heritable traits, such as DNA sequences or morphology under a model of evolution of these traits; the result of these analyses is a phylogeny – a diagrammatic hypothesis about the history of the evolutionary relationships of a group of organisms. The tips of a phylogenetic tree can be living organisms or fossils, represent the "end", or the present, in an evolutionary lineage. Phylogenetic analyses have become central to understanding biodiversity, evolution and genomes. Taxonomy is the identification and classification of organisms, it is richly informed by phylogenetics, but remains a methodologically and logically distinct discipline. The degree to which taxonomies depend on phylogenies differs depending on the school of taxonomy: phenetics ignores phylogeny altogether, trying to represent the similarity between organisms instead.
Usual methods of phylogenetic inference involve computational approaches implementing the optimality criteria and methods of parsimony, maximum likelihood, MCMC-based Bayesian inference. All these depend upon an implicit or explicit mathematical model describing the evolution of characters observed. Phenetics, popular in the mid-20th century but now obsolete, used distance matrix-based methods to construct trees based on overall similarity in morphology or other observable traits, assumed to approximate phylogenetic relationships. Prior to 1950, phylogenetic inferences were presented as narrative scenarios; such methods are ambiguous and lack explicit criteria for evaluating alternative hypotheses. The term "phylogeny" derives from the German Phylogenie, introduced by Haeckel in 1866, the Darwinian approach to classification became known as the "phyletic" approach. During the late 19th century, Ernst Haeckel's recapitulation theory, or "biogenetic fundamental law", was accepted, it was expressed as "ontogeny recapitulates phylogeny", i.e. the development of a single organism during its lifetime, from germ to adult, successively mirrors the adult stages of successive ancestors of the species to which it belongs.
But this theory has long been rejected. Instead, ontogeny evolves – the phylogenetic history of a species cannot be read directly from its ontogeny, as Haeckel thought would be possible, but characters from ontogeny can be used as data for phylogenetic analyses. 14th century, lex parsimoniae, William of Ockam, English philosopher and Franciscan friar, but the idea goes back to Aristotle, precursor concept 1763, Bayesian probability, Rev. Thomas Bayes, precursor concept 18th century, Pierre Simon first to use ML, precursor concept 1809, evolutionary theory, Philosophie Zoologique, Jean-Baptiste de Lamarck, precursor concept, foreshadowed in the 17th century and 18th century by Voltaire and Leibniz, with Leibniz proposing evolutionary changes to account for observed gaps suggesting that many species had become extinct, others transformed, different species that share common traits may have at one time been a single race foreshadowed by some early Greek philosophers such as Anaximander in the 6th century BC and the atomists of the 5th century BC, who proposed rudimentary theories of evolution 1837, Darwin's notebooks show an evolutionary tree 1843, distinction between homology and analogy, Richard Owen, precursor concept 1858, Paleontologist Heinrich Georg Bronn published a hypothetical tree to illustrating the paleontological "arrival" of new, similar species following the extinction of an older species.
Bronn did not propose a mechanism responsible for precursor concept. 1858, elaboration of evolutionary theory and Wallace in Origin of Species by Darwin the following year, precursor concept 1866, Ernst Haeckel, first publishes his phylogeny-based evolutionary tree, precursor concept 1893, Dollo's Law of Character State Irreversibility, precursor concept 1912, ML recommended and popularized by Ronald Fisher, precursor concept 1921, Tillyard uses term "phylogenetic" and distinguishes between archaic and specialized characters in his classification system 1940, term "clade" coined by Lucien Cuénot 1949, Jackknife resampling, Maurice Quenouille, precursor concept 1950, Willi Hennig's classic formalization 1952, William Wagner's groundplan divergence method 1953, "cladogenesis" coined 1960, "cladistic" coined by Cain and Harrison 1963, first attempt to use ML for phylogenetics and Cavalli-Sforza 1965 Camin-Sokal parsimony, first parsimony criterion and first computer program/algorithm for cladistic analysis both by Camin and Sokal character compatibility method called clique analysis, introduced independently by Camin and Sokal and E. O. Wilson 1966 English translation of Hennig "cladistics" and "cladogram" coined 1969 dynamic and successive wei
Animal
Animals are multicellular eukaryotic organisms that form the biological kingdom Animalia. With few exceptions, animals consume organic material, breathe oxygen, are able to move, can reproduce sexually, grow from a hollow sphere of cells, the blastula, during embryonic development. Over 1.5 million living animal species have been described—of which around 1 million are insects—but it has been estimated there are over 7 million animal species in total. Animals range in length from 8.5 millionths of a metre to 33.6 metres and have complex interactions with each other and their environments, forming intricate food webs. The category includes humans, but in colloquial use the term animal refers only to non-human animals; the study of non-human animals is known as zoology. Most living animal species are in the Bilateria, a clade whose members have a bilaterally symmetric body plan; the Bilateria include the protostomes—in which many groups of invertebrates are found, such as nematodes and molluscs—and the deuterostomes, containing the echinoderms and chordates.
Life forms interpreted. Many modern animal phyla became established in the fossil record as marine species during the Cambrian explosion which began around 542 million years ago. 6,331 groups of genes common to all living animals have been identified. Aristotle divided animals into those with those without. Carl Linnaeus created the first hierarchical biological classification for animals in 1758 with his Systema Naturae, which Jean-Baptiste Lamarck expanded into 14 phyla by 1809. In 1874, Ernst Haeckel divided the animal kingdom into the multicellular Metazoa and the Protozoa, single-celled organisms no longer considered animals. In modern times, the biological classification of animals relies on advanced techniques, such as molecular phylogenetics, which are effective at demonstrating the evolutionary relationships between animal taxa. Humans make use of many other animal species for food, including meat and eggs. Dogs have been used in hunting, while many aquatic animals are hunted for sport.
Non-human animals have appeared in art from the earliest times and are featured in mythology and religion. The word "animal" comes from the Latin animalis, having soul or living being; the biological definition includes all members of the kingdom Animalia. In colloquial usage, as a consequence of anthropocentrism, the term animal is sometimes used nonscientifically to refer only to non-human animals. Animals have several characteristics. Animals are eukaryotic and multicellular, unlike bacteria, which are prokaryotic, unlike protists, which are eukaryotic but unicellular. Unlike plants and algae, which produce their own nutrients animals are heterotrophic, feeding on organic material and digesting it internally. With few exceptions, animals breathe oxygen and respire aerobically. All animals are motile during at least part of their life cycle, but some animals, such as sponges, corals and barnacles become sessile; the blastula is a stage in embryonic development, unique to most animals, allowing cells to be differentiated into specialised tissues and organs.
All animals are composed of cells, surrounded by a characteristic extracellular matrix composed of collagen and elastic glycoproteins. During development, the animal extracellular matrix forms a flexible framework upon which cells can move about and be reorganised, making the formation of complex structures possible; this may be calcified, forming structures such as shells and spicules. In contrast, the cells of other multicellular organisms are held in place by cell walls, so develop by progressive growth. Animal cells uniquely possess the cell junctions called tight junctions, gap junctions, desmosomes. With few exceptions—in particular, the sponges and placozoans—animal bodies are differentiated into tissues; these include muscles, which enable locomotion, nerve tissues, which transmit signals and coordinate the body. There is an internal digestive chamber with either one opening or two openings. Nearly all animals make use of some form of sexual reproduction, they produce haploid gametes by meiosis.
These fuse to form zygotes, which develop via mitosis into a hollow sphere, called a blastula. In sponges, blastula larvae swim to a new location, attach to the seabed, develop into a new sponge. In most other groups, the blastula undergoes more complicated rearrangement, it first invaginates to form a gastrula with a digestive chamber and two separate germ layers, an external ectoderm and an internal endoderm. In most cases, a third germ layer, the mesoderm develops between them; these germ layers differentiate to form tissues and organs. Repeated instances of mating with a close relative during sexual reproduction leads to inbreeding depression within a population due to the increased prevalence of harmful recessive traits. Animals have evolved numerous mechanisms for avoiding close inbreeding. In some species, such as the splendid fairywren, females benefit by mating with multiple males, thus producing more offspring of higher genetic quality; some animals are capable of asexual reproduction, which results
International Union for Conservation of Nature
The International Union for Conservation of Nature is an international organization working in the field of nature conservation and sustainable use of natural resources. It is involved in data gathering and analysis, field projects and education. IUCN's mission is to "influence and assist societies throughout the world to conserve nature and to ensure that any use of natural resources is equitable and ecologically sustainable". Over the past decades, IUCN has widened its focus beyond conservation ecology and now incorporates issues related to sustainable development in its projects. Unlike many other international environmental organisations, IUCN does not itself aim to mobilize the public in support of nature conservation, it tries to influence the actions of governments and other stakeholders by providing information and advice, through building partnerships. The organization is best known to the wider public for compiling and publishing the IUCN Red List of Threatened Species, which assesses the conservation status of species worldwide.
IUCN has a membership of over 1400 non-governmental organizations. Some 16,000 scientists and experts participate in the work of IUCN commissions on a voluntary basis, it employs 1000 full-time staff in more than 50 countries. Its headquarters are in Switzerland. IUCN has observer and consultative status at the United Nations, plays a role in the implementation of several international conventions on nature conservation and biodiversity, it was involved in establishing the World Wide Fund for Nature and the World Conservation Monitoring Centre. In the past, IUCN has been criticized for placing the interests of nature over those of indigenous peoples. In recent years, its closer relations with the business sector have caused controversy. IUCN was established in 1948, it was called the International Union for the Protection of Nature and the World Conservation Union. Establishment IUCN was established on 5 October 1948, in Fontainebleau, when representatives of governments and conservation organizations signed a formal act constituting the International Union for the Protection of Nature.
The initiative to set up the new organisation came from UNESCO and from its first Director General, the British biologist Julian Huxley. The objectives of the new Union were to encourage international cooperation in the protection of nature, to promote national and international action and to compile and distribute information. At the time of its founding IUPN was the only international organisation focusing on the entire spectrum of nature conservation Early years: 1948–1956 IUPN started out with 65 members, its secretariat was located in Brussels. Its first work program focused on saving species and habitats and applying knowledge, advancing education, promoting international agreements and promoting conservation. Providing a solid scientific base for conservation action was the heart of all activities. IUPN and UNESCO were associated, they jointly organized the 1949 Conference on Protection of Nature. In preparation for this conference a list of gravely endangered species was drawn up for the first time, a precursor of the IUCN Red List of Threatened Species.
In the early years of its existence IUCN depended entirely on UNESCO funding and was forced to temporarily scale down activities when this ended unexpectedly in 1954. IUPN was successful in engaging prominent scientists and identifying important issues such as the harmful effects of pesticides on wildlife but not many of the ideas it developed were turned into action; this was caused by unwillingness to act on the part of governments, uncertainty about the IUPN mandate and lack of resources. In 1956, IUPN changed its name to International Union for Conservation of Nature and Natural Resources. Increased profile and recognition: 1956–1965 In the 1950s and 1960s Europe entered a period of economic growth and formal colonies became independent. Both developments had impact on the work of IUCN. Through the voluntary involvement of experts in its Commissions IUCN was able to get a lot of work done while still operating on a low budget, it established links with the Council of Europe. In 1961, at the request of United Nations Economic and Social Council, the United Nations Economic and Social Council, IUCN published the first global list of national parks and protected areas which it has updated since.
IUCN's best known publication, the Red Data Book on the conservation status of species, was first published in 1964. IUCN began to play a part in the development of international treaties and conventions, starting with the African Convention on the Conservation of Nature and Natural Resources. Environmental law and policy making became a new area of expertise. Africa was the focus of many of the early IUCN conservation field projects. IUCN supported the ‘Yellowstone model’ of protected area management, which restricted human presence and activity in order to protect nature. IUCN and other conservation organisations were criticized for protecting nature against people rather than with people; this model was also applied in Africa and played a role in the decision to remove the Maasai people from Serengeti National Park and the Ngorongoro Conservation Area. To establish a stable financial basis for its work, IUCN participated in setting up the World Wildlife Fund
Ireland
Ireland is an island in the North Atlantic. It is separated from Great Britain to its east by the North Channel, the Irish Sea, St George's Channel. Ireland is the second-largest island of the British Isles, the third-largest in Europe, the twentieth-largest on Earth. Politically, Ireland is divided between the Republic of Ireland, which covers five-sixths of the island, Northern Ireland, part of the United Kingdom. In 2011, the population of Ireland was about 6.6 million, ranking it the second-most populous island in Europe after Great Britain. Just under 4.8 million live in the Republic of Ireland and just over 1.8 million live in Northern Ireland. The island's geography comprises low-lying mountains surrounding a central plain, with several navigable rivers extending inland, its lush vegetation is a product of its mild but changeable climate, free of extremes in temperature. Much of Ireland was woodland until the end of the Middle Ages. Today, woodland makes up about 10% of the island, compared with a European average of over 33%, most of it is non-native conifer plantations.
There are twenty-six extant mammal species native to Ireland. The Irish climate is influenced by the Atlantic Ocean and thus moderate, winters are milder than expected for such a northerly area, although summers are cooler than those in continental Europe. Rainfall and cloud cover are abundant; the earliest evidence of human presence in Ireland is dated at 10,500 BC. Gaelic Ireland had emerged by the 1st century AD; the island was Christianised from the 5th century onward. Following the 12th century Norman invasion, England claimed sovereignty. However, English rule did not extend over the whole island until the 16th–17th century Tudor conquest, which led to colonisation by settlers from Britain. In the 1690s, a system of Protestant English rule was designed to materially disadvantage the Catholic majority and Protestant dissenters, was extended during the 18th century. With the Acts of Union in 1801, Ireland became a part of the United Kingdom. A war of independence in the early 20th century was followed by the partition of the island, creating the Irish Free State, which became sovereign over the following decades, Northern Ireland, which remained a part of the United Kingdom.
Northern Ireland saw much civil unrest from the late 1960s until the 1990s. This subsided following a political agreement in 1998. In 1973 the Republic of Ireland joined the European Economic Community while the United Kingdom, Northern Ireland, as part of it, did the same. Irish culture has had a significant influence on other cultures in the field of literature. Alongside mainstream Western culture, a strong indigenous culture exists, as expressed through Gaelic games, Irish music and the Irish language; the island's culture shares many features with that of Great Britain, including the English language, sports such as association football, horse racing, golf. The names Éire derive from Old Irish Eriu; this in turn comes from the Proto-Celtic *Iveriu, the source of Latin Hibernia. Iveriu derives from a root meaning'fat, prosperous'. During the last glacial period, up until about 10,000 BC, most of Ireland was periodically covered in ice. Sea levels were lower and Ireland, like Great Britain, formed part of continental Europe.
By 16,000 BC, rising sea levels due to ice melting caused Ireland to become separated from Great Britain. Around 6000 BC, Great Britain itself became separated from continental Europe; the earliest evidence of human presence in Ireland is dated at 10,500 BC, demonstrated by a butchered bear bone found in a cave in County Clare. It is not until about 8000 BC, that more sustained occupation of the island has been shown, with evidence for Mesolithic communities around the island; these Mesolithic communities lived as hunter-gatherers across the island until about 4000 BC. Some time before 4000 BC, Neolithic settlers arrived introducing cereal cultivars, domesticated animals such as cattle and sheep, large timber building, stone monuments; the earliest evidence for farming in Ireland or Great Britain is from Co.. Kerry, where a flint knife, cattle bones and a sheep's tooth were carbon-dated to c. 4350 BC. Field systems were developed in different parts of Ireland, including at the Céide Fields, preserved beneath a blanket of peat in present-day Tyrawley.
An extensive field system, arguably the oldest in the world, consisted of small divisions separated by dry-stone walls. The fields were farmed for several centuries between 3500 BC and 3000 BC. Wheat and barley were the principal crops; the Bronze Age – defined by the use of metal – began around 2500 BC, with technology changing people's everyday lives during this period through innovations such as the wheel. According to John T. Koch and others, Ireland in the Late Bronze Age was part of a maritime trading-network culture called the Atlantic Bronze Age that included Britain, western France and Iberia, that this is where Celtic languages developed; this contrasts with the traditional view that their origin lies in mainland Europe with the Hallstatt culture. During the Iron Age, a Celtic language and culture emerged in Ireland. How and when the island became Celtic has been debated for close to a century, with the migrations of the Celts being one of the more enduring themes of archaeological and linguistic studies.
The most recent genetic research s
Chordate
A chordate is an animal constituting the phylum Chordata. During some period of their life cycle, chordates possess a notochord, a dorsal nerve cord, pharyngeal slits, an endostyle, a post-anal tail: these five anatomical features define this phylum. Chordates are bilaterally symmetric; the Chordata and Ambulacraria together form the superphylum Deuterostomia. Chordates are divided into three subphyla: Vertebrata. There are extinct taxa such as the Vetulicolia. Hemichordata has been presented as a fourth chordate subphylum, but now is treated as a separate phylum: hemichordates and Echinodermata form the Ambulacraria, the sister phylum of the Chordates. Of the more than 65,000 living species of chordates, about half are bony fish that are members of the superclass Osteichthyes. Chordate fossils have been found from as early as the Cambrian explosion, 541 million years ago. Cladistically, vertebrates - chordates with the notochord replaced by a vertebral column during development - are considered to be a subgroup of the clade Craniata, which consists of chordates with a skull.
The Craniata and Tunicata compose the clade Olfactores. Chordates form a phylum of animals that are defined by having at some stage in their lives all of the following anatomical features: A notochord, a stiff rod of cartilage that extends along the inside of the body. Among the vertebrate sub-group of chordates the notochord develops into the spine, in wholly aquatic species this helps the animal to swim by flexing its tail. A dorsal neural tube. In fish and other vertebrates, this develops into the spinal cord, the main communications trunk of the nervous system. Pharyngeal slits; the pharynx is the part of the throat behind the mouth. In fish, the slits are modified to form gills, but in some other chordates they are part of a filter-feeding system that extracts particles of food from the water in which the animals live. Post-anal tail. A muscular tail that extends backwards behind the anus. An endostyle; this is a groove in the ventral wall of the pharynx. In filter-feeding species it produces mucus to gather food particles, which helps in transporting food to the esophagus.
It stores iodine, may be a precursor of the vertebrate thyroid gland. There are soft constraints that separate chordates from certain other biological lineages, but are not part of the formal definition: All chordates are deuterostomes; this means. All chordates are based on a bilateral body plan. All chordates are coelomates, have a fluid filled body cavity called a coelom with a complete lining called peritoneum derived from mesoderm; the following schema is from the third edition of Vertebrate Palaeontology. The invertebrate chordate classes are from Fishes of the World. While it is structured so as to reflect evolutionary relationships, it retains the traditional ranks used in Linnaean taxonomy. Phylum Chordata †Vetulicolia? Subphylum Cephalochordata – Class Leptocardii Clade Olfactores Subphylum Tunicata – Class Ascidiacea Class Thaliacea Class Appendicularia Class Sorberacea Subphylum Vertebrata Infraphylum incertae sedis Cyclostomata Superclass'Agnatha' paraphyletic Class Myxini Class Petromyzontida or Hyperoartia Class †Conodonta Class †Myllokunmingiida Class †Pteraspidomorphi Class †Thelodonti Class †Anaspida Class †Cephalaspidomorphi Infraphylum Gnathostomata Class †Placodermi Class Chondrichthyes Class †Acanthodii Superclass Osteichthyes Class Actinopterygii Class Sarcopterygii Superclass Tetrapoda Class Amphibia Class Sauropsida Class Synapsida Craniates, one of the three subdivisions of chordates, all have distinct skulls.
They include the hagfish. Michael J. Benton commented that "craniates are characterized by their heads, just as chordates, or all deuterostomes, are by their tails". Most craniates are vertebrates; these consist of a series of bony or cartilaginous cylindrical vertebrae with neural arches that protect the spinal cord, with projections that link the vertebrae. However hagfish have incomplete braincases and no vertebrae, are therefore not regarded as vertebrates, but as members of the craniates, the group from which vertebrates are thought to have evolved; however the cladistic exclusion of hagfish from the vertebrates is controversial, as they ma
Oxford English Dictionary
The Oxford English Dictionary is the principal historical dictionary of the English language, published by Oxford University Press. It traces the historical development of the English language, providing a comprehensive resource to scholars and academic researchers, as well as describing usage in its many variations throughout the world; the second edition, comprising 21,728 pages in 20 volumes, was published in 1989. Work began on the dictionary in 1857, but it was only in 1884 that it began to be published in unbound fascicles as work continued on the project, under the name of A New English Dictionary on Historical Principles. In 1895, the title The Oxford English Dictionary was first used unofficially on the covers of the series, in 1928 the full dictionary was republished in ten bound volumes. In 1933, the title The Oxford English Dictionary replaced the former name in all occurrences in its reprinting as twelve volumes with a one-volume supplement. More supplements came over the years until 1989.
Since 2000, compilation of a third edition of the dictionary has been underway half of, complete. The first electronic version of the dictionary was made available in 1988; the online version has been available since 2000, as of April 2014 was receiving over two million hits per month. The third edition of the dictionary will most only appear in electronic form: the Chief Executive of Oxford University Press has stated that it is unlikely that it will be printed; as a historical dictionary, the Oxford English Dictionary explains words by showing their development rather than their present-day usages. Therefore, it shows definitions in the order that the sense of the word began being used, including word meanings which are no longer used; each definition is shown with numerous short usage quotations. This allows the reader to get an approximate sense of the time period in which a particular word has been in use, additional quotations help the reader to ascertain information about how the word is used in context, beyond any explanation that the dictionary editors can provide.
The format of the OED's entries has influenced numerous other historical lexicography projects. The forerunners to the OED, such as the early volumes of the Deutsches Wörterbuch, had provided few quotations from a limited number of sources, whereas the OED editors preferred larger groups of quite short quotations from a wide selection of authors and publications; this influenced volumes of this and other lexicographical works. According to the publishers, it would take a single person 120 years to "key in" the 59 million words of the OED second edition, 60 years to proofread them, 540 megabytes to store them electronically; as of 30 November 2005, the Oxford English Dictionary contained 301,100 main entries. Supplementing the entry headwords, there are 157,000 bold-type derivatives; the dictionary's latest, complete print edition was printed in 20 volumes, comprising 291,500 entries in 21,730 pages. The longest entry in the OED2 was for the verb set, which required 60,000 words to describe some 430 senses.
As entries began to be revised for the OED3 in sequence starting from M, the longest entry became make in 2000 put in 2007 run in 2011. Despite its considerable size, the OED is neither the world's largest nor the earliest exhaustive dictionary of a language. Another earlier large dictionary is the Grimm brothers' dictionary of the German language, begun in 1838 and completed in 1961; the first edition of the Vocabolario degli Accademici della Crusca is the first great dictionary devoted to a modern European language and was published in 1612. The official dictionary of Spanish is the Diccionario de la lengua española, its first edition was published in 1780; the Kangxi dictionary of Chinese was published in 1716. The dictionary began as a Philological Society project of a small group of intellectuals in London: Richard Chenevix Trench, Herbert Coleridge, Frederick Furnivall, who were dissatisfied with the existing English dictionaries; the Society expressed interest in compiling a new dictionary as early as 1844, but it was not until June 1857 that they began by forming an "Unregistered Words Committee" to search for words that were unlisted or poorly defined in current dictionaries.
In November, Trench's report was not a list of unregistered words. The Society realized that the number of unlisted words would be far more than the number of words in the English dictionaries of the 19th century, shifted their idea from covering only words that were not in English diction
