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
In biology, taxonomy is the science of defining and naming groups of biological organisms on the basis of shared characteristics. Organisms are grouped together into taxa and these groups are given a taxonomic rank; the principal ranks in modern use are domain, phylum, order, family and species. The Swedish botanist Carl Linnaeus is regarded as the founder of the current system of taxonomy, as he developed a system known as Linnaean taxonomy for categorizing organisms and binomial nomenclature for naming organisms. With the advent of such fields of study as phylogenetics and systematics, the Linnaean system has progressed to a system of modern biological classification based on the evolutionary relationships between organisms, both living and extinct; the exact definition of taxonomy varies from source to source, but the core of the discipline remains: the conception and classification of groups of organisms. As points of reference, recent definitions of taxonomy are presented below: Theory and practice of grouping individuals into species, arranging species into larger groups, giving those groups names, thus producing a classification.
A field of science that encompasses description, identification and classification The science of classification, in biology the arrangement of organisms into a classification "The science of classification as applied to living organisms, including study of means of formation of species, etc." "The analysis of an organism's characteristics for the purpose of classification" "Systematics studies phylogeny to provide a pattern that can be translated into the classification and names of the more inclusive field of taxonomy" The varied definitions either place taxonomy as a sub-area of systematics, invert that relationship, or appear to consider the two terms synonymous. There is some disagreement as to whether biological nomenclature is considered a part of taxonomy, or a part of systematics outside taxonomy. For example, definition 6 is paired with the following definition of systematics that places nomenclature outside taxonomy: Systematics: "The study of the identification and nomenclature of organisms, including the classification of living things with regard to their natural relationships and the study of variation and the evolution of taxa".
A whole set of terms including taxonomy, systematic biology, biosystematics, scientific classification, biological classification, phylogenetics have at times had overlapping meanings – sometimes the same, sometimes different, but always related and intersecting. The broadest meaning of "taxonomy" is used here; the term itself was introduced in 1813 by de Candolle, in his Théorie élémentaire de la botanique. A taxonomic revision or taxonomic review is a novel analysis of the variation patterns in a particular taxon; this analysis may be executed on the basis of any combination of the various available kinds of characters, such as morphological, palynological and genetic. A monograph or complete revision is a revision, comprehensive for a taxon for the information given at a particular time, for the entire world. Other revisions may be restricted in the sense that they may only use some of the available character sets or have a limited spatial scope. A revision results in a conformation of or new insights in the relationships between the subtaxa within the taxon under study, which may result in a change in the classification of these subtaxa, the identification of new subtaxa, or the merger of previous subtaxa.
The term "alpha taxonomy" is used today to refer to the discipline of finding and naming taxa species. In earlier literature, the term had a different meaning, referring to morphological taxonomy, the products of research through the end of the 19th century. William Bertram Turrill introduced the term "alpha taxonomy" in a series of papers published in 1935 and 1937 in which he discussed the philosophy and possible future directions of the discipline of taxonomy. … there is an increasing desire amongst taxonomists to consider their problems from wider viewpoints, to investigate the possibilities of closer co-operation with their cytological and genetical colleagues and to acknowledge that some revision or expansion of a drastic nature, of their aims and methods, may be desirable … Turrill has suggested that while accepting the older invaluable taxonomy, based on structure, conveniently designated "alpha", it is possible to glimpse a far-distant taxonomy built upon as wide a basis of morphological and physiological facts as possible, one in which "place is found for all observational and experimental data relating if indirectly, to the constitution, subdivision and behaviour of species and other taxonomic groups".
Ideals can, it may be said, never be realized. They have, however, a great value of acting as permanent stimulants, if we have some vague, ideal of an "omega" taxonomy we may progress a little way down the Greek alphabet; some of us please ourselves by thinking. Turrill thus explicitly excludes from alpha taxonomy various areas of study that he includes within taxonomy as a whole, such as ecology, physiology and cytology, he further excludes phylogenetic reconstruction from alp
National Center for Biotechnology Information
The National Center for Biotechnology Information is part of the United States National Library of Medicine, a branch of the National Institutes of Health. The NCBI is located in Bethesda and was founded in 1988 through legislation sponsored by Senator Claude Pepper; the NCBI houses a series of databases relevant to biotechnology and biomedicine and is an important resource for bioinformatics tools and services. Major databases include GenBank for DNA sequences and PubMed, a bibliographic database for the biomedical literature. Other databases include the NCBI Epigenomics database. All these databases are available online through the Entrez search engine. NCBI was directed by David Lipman, one of the original authors of the BLAST sequence alignment program and a respected figure in bioinformatics, he led an intramural research program, including groups led by Stephen Altschul, David Landsman, Eugene Koonin, John Wilbur, Teresa Przytycka, Zhiyong Lu. David Lipman stood down from his post in May 2017.
NCBI has had responsibility for making available the GenBank DNA sequence database since 1992. GenBank coordinates with individual laboratories and other sequence databases such as those of the European Molecular Biology Laboratory and the DNA Data Bank of Japan. Since 1992, NCBI has grown to provide other databases in addition to GenBank. NCBI provides Gene, Online Mendelian Inheritance in Man, the Molecular Modeling Database, dbSNP, the Reference Sequence Collection, a map of the human genome, a taxonomy browser, coordinates with the National Cancer Institute to provide the Cancer Genome Anatomy Project; the NCBI assigns a unique identifier to each species of organism. The NCBI has software tools that are available by WWW browsing or by FTP. For example, BLAST is a sequence similarity searching program. BLAST can do sequence comparisons against the GenBank DNA database in less than 15 seconds; the "NCBI Bookshelf is a collection of accessible, downloadable, on-line versions of selected biomedical books.
The Bookshelf covers a wide range of topics including molecular biology, cell biology, microbiology, disease states from a molecular and cellular point of view, research methods, virology. Some of the books are online versions of published books, while others, such as Coffee Break, are written and edited by NCBI staff; the Bookshelf is a complement to the Entrez PubMed repository of peer-reviewed publication abstracts in that Bookshelf contents provide established perspectives on evolving areas of study and a context in which many disparate individual pieces of reported research can be organized. BLAST is an algorithm used for calculating sequence similarity between biological sequences such as nucleotide sequences of DNA and amino acid sequences of proteins. BLAST is a powerful tool for finding sequences similar to the query sequence within the same organism or in different organisms, it searches the query sequence on NCBI databases and servers and post the results back to the person's browser in chosen format.
Input sequences to the BLAST are in FASTA or Genbank format while output could be delivered in variety of formats such as HTML, XML formatting and plain text. HTML is the default output format for NCBI's web-page. Results for NCBI-BLAST are presented in graphical format with all the hits found, a table with sequence identifiers for the hits having scoring related data, along with the alignments for the sequence of interest and the hits received with analogous BLAST scores for these The Entrez Global Query Cross-Database Search System is used at NCBI for all the major databases such as Nucleotide and Protein Sequences, Protein Structures, PubMed, Complete Genomes, OMIM, several others. Entrez is both indexing and retrieval system having data from various sources for biomedical research. NCBI distributed the first version of Entrez in 1991, composed of nucleotide sequences from PDB and GenBank, protein sequences from SWISS-PROT, translated GenBank, PIR, PRF, PDB and associated abstracts and citations from PubMed.
Entrez is specially designed to integrate the data from several different sources and formats into a uniform information model and retrieval system which can efficiently retrieve that relevant references and structures. Gene has been implemented at NCBI to organize the information about genes, it serves as a major node in the nexus of genomic map, sequence, protein function and homology data. A unique GeneID is assigned to each gene record. Gene records for known or predicted genes are established here and are demarcated by map positions or nucleotide sequence. Gene has several advantages over its predecessor, LocusLink, better integration with other databases in NCBI, broader taxonomic scope, enhanced options for query and retrieval provided by Entrez system. Protein database maintains the text record for individual protein sequences, derived from many different resources such as NCBI Reference Sequence project, GenbBank, PDB and UniProtKB/SWISS-Prot. Protein records are present in different formats including FASTA and XML and are linked to other NCBI resources.
Protein provides the relevant data to the users such as genes, DNA/RNA sequences, biological pathways and variation data and literature. It provides the pre-determined sets of similar and identical proteins for each sequence as computed by the BLAST; the Structure database of NCBI contains 3D coordinate sets for experimentally-determined structures in PDB that are imported by NCBI. The Conserved Domain database of pro
Northern blue-tongued skink
The northern blue-tongued skink is the largest and heaviest of the blue-tongued lizards. They are native to Australia and found exclusively in the Northern Region, they live around 20 years and are kept as pets. The northern blue-tongued skink is a subspecies of the eastern blue-tongued lizard. Similar to other blue-tongued lizards, the northern blue-tongued skink has distinctive patterning. Northerns tend to be a bright orange to soft peachy orange or a yellowish colour with darker stripes along their sides and backs, with a lighter, creamier colour on their bellies, they have bright blue tongues used to warn off or startle predators. Their legs are small compared to the length and width of their bodies, they grow to about 22 inches in total length. The breeding season occurs once yearly; when a male finds a suitable female, he follows her. Mating is aggressive and the male holds the female down by biting her. Damage to the scales and light bleeding are common; this is the only time. Northern blue-tongued skinks are ovoviviparous.
Their gestation period is 100 days with 4 - 6 young born per litter. The offspring look the same as the adults with only slight variations to colouring, they begin eating small insects and fruit a few days after birth. Seike Reptiles Honolulu Zoo
The Reptile Database is a scientific database that collects taxonomic information on all living reptile species. The database focuses on species and has entries for all recognized ~13,000 species and their subspecies, although there is a lag time of up to a few months before newly described species become available online; the database collects scientific and common names, literature references, distribution information, type information and other taxonomically relevant information. The database was founded in 1995 as EMBL Reptile Database when the founder, Peter Uetz, was a graduate student at the European Molecular Biology Laboratory in Heidelberg, Germany. Thure Etzold had developed the first web interface for the EMBL DNA sequence database, used as interface for the Reptile Database. In 2006 the database moved to The Institute of Genomic Research and operated as TIGR Reptile Database until TIGR was merged into the J Craig Venter Institute where Uetz was an Associate Professor until 2010.
Since 2010 the database has been maintained on servers in the Czech Republic under the supervision of Peter Uetz and Jirí Hošek, a Czech programmer. As of March 2018, the Reptile Database lists about 10,700 species in about 1180 genera, has about 45,000 literature references and about 11,000 photos; the database has grown since its inception with an average of ~120 new species described per year over the preceding decade. The Reptile Database has been a member of the Species 2000 project that has produced the Catalogue of Life, a meta-database of more than 150 species databases that catalog all living species on the planet; the CoL provides taxonomic information to the Encyclopedia of Life. The Reptile Database collaborates with the World Register of Marine Species, the citizen science project iNaturalist, has links to the IUCN Redlist database; the NCBI taxonomy database links out to the Reptile Database. The Reptile Database—Home Page Reptile Database Search—Search page at Reptarium
INaturalist is a citizen science project and online social network of naturalists, citizen scientists, biologists built on the concept of mapping and sharing observations of biodiversity across the globe. INaturalist may be accessed from its mobile applications. Observations recorded with iNaturalist provide valuable open data to scientific research projects, conservation agencies, other organizations, the public; the project has been called "a standard-bearer for natural history mobile applications." INaturalist.org began in 2008 as a UC Berkeley School of Information Master's final project of Nate Agrin, Jessica Kline, Ken-ichi Ueda. Nate Agrin and Ken-ichi Ueda continued work on the site with a web developer. In 2011, Ueda began collaboration with Scott Loarie, a research fellow at Stanford University and lecturer at UC Berkeley. Ueda and Loarie are the current co-directors of iNaturalist.org. The organization merged with the California Academy of Sciences on April 24, 2014. In 2014, iNaturalist celebrated its one millionth observation.
In 2017, iNaturalist became a joint initiative between the California Academy of Sciences and the National Geographic Society. The iNaturalist platform is based on crowdsourcing of data. An iNaturalist observation records an encounter with an individual organism at a particular time and place. In addition to recording actual audio and photos of the organism, an iNaturalist observation may record evidence of an organism, such as animal tracks and scat, but the scope of iNaturalist excludes natural but inert subjects such as geologic or hydrologic features. Users upload photos as evidence of their findings, though audio recordings are accepted and such evidence is not a strict requirement. Users may share observation locations publicly, "obscure" them to display a less precise location, or make the locations private. On iNaturalist, other users add identifications to each other's observations in order to confirm or improve the "community identification." Observations are classified as "casual," "needs ID", or "research grade" based on the quality of the data provided and the community identification process.
"Research grade" observations are incorporated into other online databases such as The Global Biodiversity Information Facility. Users have the option to license their observations and audio recordings in several ways, including for the public domain, Creative Commons, or with all rights reserved. In addition to observations being identified by others in the community, iNaturalist includes an automated species identification computer vision tool. Images can be identified via an artificial intelligence model, trained on the large database of the "research grade" observations on iNaturalist. A broader taxon such as a genus or family is provided if the model cannot decide what the species is. If the image has poor lighting, is blurry, or contains multiple subjects, it can be difficult for the model to determine the species and it may decide incorrectly. Multiple species suggestions are provided; as of 4 October 2018, iNaturalist users contributed over 15,900,000 observations of plants and other organisms worldwide, with over 88,000 users active in the previous 30 days.
INaturalist is the preferred application for crowd-sourced biodiversity data in Mexico and southern Africa. Users have contributed to thousands of different projects on iNaturalist; the platform is used to record observations during bioblitzes, which are biological surveying events that attempt to record all the species that occur within a designated area, a specific project type on iNaturalist. Other project types include collections of observations by location or taxon, or documenting specific types of observations such as animal tracks and signs, the spread of invasive species, fishing catches, or discovering new species. In 2011, iNaturalist was used as a platform to power the Global Amphibian and Global Reptile BioBlitzes, in which observations were used to help monitor the occurrence and distribution of the world's reptiles and amphibian species; the US National Park Service partnered with iNaturalist to record observations from the 2016 National Parks BioBlitz. That project exceeded 100,000 observations in August 2016.
In 2017, the United Nations Environment Programme teamed up with iNaturalist to celebrate World Environment Day. The City Nature Challenge In 2016, Lila Higgins from the Natural History Museum of Los Angeles County and Alison Young from the California Academy of Sciences co-founded the City Nature Challenge. In the first City Nature Challenge, naturalists in Los Angeles and the San Francisco Bay Area documented over 20,000 observations with the iNaturalist platform. In 2017, the challenge expanded to 16 cities across the United States and collected over 125,000 observations of wildlife in 5 days. In 2018, the challenge expanded to a global audience, with 68 cities participating from 19 countries, with some cities using community science platforms other than iNaturalist to participate. In 4 days, over 17,000 people cataloged over 440,000 nature observations in urban regions around the world. Users can access iNaturalist data or add their observations to iNaturalist in several ways: via the iNaturalist.org website, through two apps: iNaturalist and Seek, or through partner organizations such as the Global Biodiversity Information Facility website.
On the primary iNaturalist app, users can contribute nature observations to the public, online dataset, though on Seek, designed for children and families, no online account r
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