|Description||Tree of Life Web Project|
|Authors||David Maddison, Katja-Sabine Schulz, and Wayne Maddison|
The Tree of Life Web Project is an Internet project providing information about the diversity and phylogeny of life on Earth.
The Internet is the global system of interconnected computer networks that use the Internet protocol suite (TCP/IP) to link devices worldwide. It is a network of networks that consists of private, public, academic, business, and government networks of local to global scope, linked by a broad array of electronic, wireless, and optical networking technologies. The Internet carries a vast range of information resources and services, such as the inter-linked hypertext documents and applications of the World Wide Web (WWW), electronic mail, telephony, and file sharing.
Biodiversity is the variety and variability of life on Earth. Biodiversity is typically a measure of variation at the genetic, species, and ecosystem level. Terrestrial biodiversity is usually greater near the equator, which is the result of the warm climate and high primary productivity. Biodiversity is not distributed evenly on Earth, and is richest in the tropics. These tropical forest ecosystems cover less than 10 percent of earth's surface, and contain about 90 percent of the world's species. Marine biodiversity is usually highest along coasts in the Western Pacific, where sea surface temperature is highest, and in the mid-latitudinal band in all oceans. There are latitudinal gradients in species diversity. Biodiversity generally tends to cluster in hotspots, and has been increasing through time, but will be likely to slow in the future.
Life is a characteristic that distinguishes physical entities that have biological processes, such as signaling and self-sustaining processes, from those that do not, either because such functions have ceased, or because they never had such functions and are classified as inanimate. Various forms of life exist, such as plants, animals, fungi, protists, archaea, and bacteria. The criteria can at times be ambiguous and may or may not define viruses, viroids, or potential synthetic life as "living". Biology is the science concerned with the study of life.
This collaborative peer reviewed project began in 1995, and is written by biologists from around the world. The site has not been updated since 2011, however the pages are still accessible.
Peer review is the evaluation of work by one or more people with similar competences as the producers of the work (peers). It functions as a form of self-regulation by qualified members of a profession within the relevant field. Peer review methods are used to maintain quality standards, improve performance, and provide credibility. In academia, scholarly peer review is often used to determine an academic paper's suitability for publication. Peer review can be categorized by the type of activity and by the field or profession in which the activity occurs, e.g., medical peer review.
A biologist is a scientist who has specialized knowledge in the field of biology, the scientific study of life. Biologists involved in fundamental research attempt to explore and further explain the underlying mechanisms that govern the functioning of living matter. Biologists involved in applied research attempt to develop or improve more specific processes and understanding, in fields such as medicine and industry.
The pages are linked hierarchically, in the form of the branching evolutionary tree of life, organized cladistically.Each page contains information about one particular group of organisms and is organized according to a branched tree-like form, thus showing hypothetical relationships between different groups of organisms.
A hierarchy is an arrangement of items in which the items are represented as being "above", "below", or "at the same level as" one another. Hierarchy is an important concept in a wide variety of fields, such as philosophy, mathematics, computer science, organizational theory, systems theory, and the social sciences.
Evolution is change in the heritable characteristics of biological populations over successive generations. These characteristics are the expressions of genes that are passed on from parent to offspring during reproduction. Different characteristics tend to exist within any given population as a result of mutation, genetic recombination and other sources of genetic variation. Evolution occurs when evolutionary processes such as natural selection and genetic drift act on this variation, resulting in certain characteristics becoming more common or rare within a population. It is this process of evolution that has given rise to biodiversity at every level of biological organisation, including the levels of species, individual organisms and molecules.
Cladistics is an approach to biological classification in which organisms are categorized in groups ("clades") based on the most recent common ancestor. Hypothesized relationships are typically based on shared derived characteristics (synapomorphies) that can be traced to the most recent common ancestor and are not present in more distant groups and ancestors. A key feature of a clade is that a common ancestor and all its descendants are part of the clade. Importantly, all descendants stay in their overarching ancestral clade. For example, if within a strict cladistic framework the terms animals, bilateria/worms, fishes/vertebrata, or monkeys/anthropoidea were used, these terms would include humans. Many of these terms are normally used paraphyletically, outside of cladistics, e.g. as a 'grade'. Radiation results in the generation of new subclades by bifurcation.
In 2009 the project ran into funding problems from the University of Arizona. Pages and Treehouses submitted took a considerably longer time to be approved as they were being reviewed by a small group of volunteers, and apparently, around 2011, all activities ended.
The University of Arizona is a public research university in Tucson, Arizona. Founded in 1885, the UA was the first university in the Arizona Territory. As of 2018, the university enrolls 45,217 students in 19 separate colleges/schools, including the University of Arizona College of Medicine in Tucson and Phoenix and the James E. Rogers College of Law, and is affiliated with two academic medical centers. The University of Arizona is governed by the Arizona Board of Regents. The University of Arizona is one of the elected members of the Association of American Universities and is the only representative from the state of Arizona to this group.
The idea of this project started in the late 1980s. David Maddison was working on a computer program MacClade during his PhD research. This is an application that give insight into species' phylogenetic trees. He wanted to extend this program with a feature that allowed the user to browse through phylogenetic trees and zoom into other lower or higher taxa.
A Doctor of Philosophy is the highest university degree that is conferred after a course of study by universities in most countries. PhDs are awarded for programs across the whole breadth of academic fields. As an earned research degree, those studying for a PhD are usually required to produce original research that expands the boundaries of knowledge, normally in the form of a thesis or dissertation, and defend their work against experts in the field. The completion of a PhD is often a requirement for employment as a university professor, researcher, or scientist in many fields. Individuals who have earned a Doctor of Philosophy degree may, in many jurisdictions, use the title Doctor or, in non-English-speaking countries, variants such as "Dr. phil." with their name, although the proper etiquette associated with this usage may also be subject to the professional ethics of their own scholarly field, culture, or society. Those who teach at universities or work in academic, educational, or research fields are usually addressed by this title "professionally and socially in a salutation or conversation." Alternatively, holders may use post-nominal letters such as "Ph.D.", "PhD", or "DPhil". It is, however, considered incorrect to use both the title and post-nominals at the same time.
Hence, this association was not unique in a stand-alone application. The researchers came up with the idea to export the application into the world wide web and this was realized in 1995. From 1996-2011, over 300 biologists from around the globe added taxa web pages into the phylogeny browser.
To ensure the quality of ToL project, the board made use of peer-review. The pages that were reviewed were sent to two or three researchers that specialized in the particular subject.It is possible to visit the personal page of the author. If this is not accessible then the institution is always at the footnote.
A clade, also known as monophyletic group, is a group of organisms that consists of a common ancestor and all its lineal descendants, and represents a single "branch" on the "tree of life". Rather than the English term, the equivalent Latin term cladus is often used in taxonomical literature.
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, and represent the 'end', or the present, in an evolutionary lineage. A phylogenetic tree can be rooted or unrooted. A rooted tree indicates the common ancestor, or ancestral lineage, of the tree. An unrooted tree makes no assumption about the ancestral line, and does not show the origin or "root" of the gene or organism in question. Phylogenetic analyses have become central to understanding biodiversity, evolution, ecology, and genomes.
Biological systematics is the study of the diversification of living forms, both past and present, and the relationships among living things through time. Relationships are visualized as evolutionary trees. Phylogenies have two components: branching order and branch length. Phylogenetic trees of species and higher taxa are used to study the evolution of traits and the distribution of organisms (biogeography). Systematics, in other words, is used to understand the evolutionary history of life on Earth.
In biology, taxonomy is the science of naming, defining (circumscribing) and classifying groups of biological organisms on the basis of shared characteristics. Organisms are grouped together into taxa and these groups are given a taxonomic rank; groups of a given rank can be aggregated to form a super-group of higher rank, thus creating a taxonomic hierarchy. The principal ranks in modern use are domain, kingdom, phylum, class, order, family, genus, 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.
A cladogram is a diagram used in cladistics to show relations among organisms. A cladogram is not, however, an evolutionary tree because it does not show how ancestors are related to descendants, nor does it show how much they have changed; nevertheless, many evolutionary trees can be inferred from a single cladogram. A cladogram uses lines that branch off in different directions ending at a clade, a group of organisms with a last common ancestor. There are many shapes of cladograms but they all have lines that branch off from other lines. The lines can be traced back to where they branch off. These branching off points represent a hypothetical ancestor which can be inferred to exhibit the traits shared among the terminal taxa above it. This hypothetical ancestor might then provide clues about the order of evolution of various features, adaptation, and other evolutionary narratives about ancestors. Although traditionally such cladograms were generated largely on the basis of morphological characters, DNA and RNA sequencing data and computational phylogenetics are now very commonly used in the generation of cladograms, either on their own or in combination with morphology.
A phylogenetic tree or evolutionary tree is a branching diagram or "tree" showing the evolutionary relationships among various biological species or other entities—their phylogeny —based upon similarities and differences in their physical or genetic characteristics. All life on Earth is part of a single phylogenetic tree, indicating common ancestry.
Molecular phylogenetics is the branch of phylogeny that analyzes genetic, hereditary molecular differences, predominately in DNA sequences, to gain information on an organism's evolutionary relationships. From these analyses, it is possible to determine the processes by which diversity among species has been achieved. The result of a molecular phylogenetic analysis is expressed in a phylogenetic tree. Molecular phylogenetics is one aspect of molecular systematics, a broader term that also includes the use of molecular data in taxonomy and biogeography.
Phylogenesis is the biological process by which a taxon appears. The science that studies these processes is called phylogenetics.
Evolutionary taxonomy, evolutionary systematics or Darwinian classification is a branch of biological classification that seeks to classify organisms using a combination of phylogenetic relationship, progenitor-descendant relationship, and degree of evolutionary change. This type of taxonomy may consider whole taxa rather than single species, so that groups of species can be inferred as giving rise to new groups. The concept found its most well-known form in the modern evolutionary synthesis of the early 1940s.
In cladistics or phylogenetics, an outgroup is a more distantly related group of organisms that serves as a reference group when determining the evolutionary relationships of the ingroup, the set of organisms under study, and is distinct from sociological outgroups. The outgroup is used as a point of comparison for the ingroup and specifically allows for the phylogeny to be rooted. Because the polarity (direction) of character change can be determined only on a rooted phylogeny, the choice of outgroup is essential for understanding the evolution of traits along a phylogeny.
In phylogenetics, maximum parsimony is an optimality criterion under which the phylogenetic tree that minimizes the total number of character-state changes is to be preferred. Under the maximum-parsimony criterion, the optimal tree will minimize the amount of homoplasy. In other words, under this criterion, the shortest possible tree that explains the data is considered best. The principle is akin to Occam's razor, which states that—all else being equal—the simplest hypothesis that explains the data should be selected. Some of the basic ideas behind maximum parsimony were presented by James S. Farris in 1970 and Walter M. Fitch in 1971.
In phylogenetics, long branch attraction (LBA) is a form of systematic error whereby distantly related lineages are incorrectly inferred to be closely related. LBA arises when the amount of molecular or morphological change accumulated within a lineage is sufficient to cause that lineage to appear similar to another long-branched lineage, solely because they have both undergone a large amount of change, rather than because they are related by descent. Such bias is more common when the overall divergence of some taxa results in long branches within a phylogeny. Long-branches are often attracted to the base of a phylogenetic tree, because the lineage included to represent an outgroup is often also long-branched. The frequency of true LBA is unclear and often debated, and some authors view it as untestable and therefore irrelevant to empirical phylogenetic inference. Although often viewed as a failing of parsimony-based methodology, LBA could in principle result from a variety of scenarios and be inferred under multiple analytical paradigms.
In alpha taxonomy, a grade is a taxon united by a level of morphological or physiological complexity. The term was coined by British biologist Julian Huxley, to contrast with clade, a strictly phylogenetic unit.
Computational phylogenetics is the application of computational algorithms, methods, and programs to phylogenetic analyses. The goal is to assemble a phylogenetic tree representing a hypothesis about the evolutionary ancestry of a set of genes, species, or other taxa. For example, these techniques have been used to explore the family tree of hominid species and the relationships between specific genes shared by many types of organisms. Traditional phylogenetics relies on morphological data obtained by measuring and quantifying the phenotypic properties of representative organisms, while the more recent field of molecular phylogenetics uses nucleotide sequences encoding genes or amino acid sequences encoding proteins as the basis for classification. Many forms of molecular phylogenetics are closely related to and make extensive use of sequence alignment in constructing and refining phylogenetic trees, which are used to classify the evolutionary relationships between homologous genes represented in the genomes of divergent species. The phylogenetic trees constructed by computational methods are unlikely to perfectly reproduce the evolutionary tree that represents the historical relationships between the species being analyzed. The historical species tree may also differ from the historical tree of an individual homologous gene shared by those species.
Phylogenetic comparative methods (PCMs) use information on the historical relationships of lineages (phylogenies) to test evolutionary hypotheses. The comparative method has a long history in evolutionary biology; indeed, Charles Darwin used differences and similarities between species as a major source of evidence in The Origin of Species. However, the fact that closely related lineages share many traits and trait combinations as a result of the process of descent with modification means that lineages are not independent. This realization inspired the development of explicitly phylogenetic comparative methods. Initially, these methods were primarily developed to control for phylogenetic history when testing for adaptation; however, in recent years the use of the term has broadened to include any use of phylogenies in statistical tests. Although most studies that employ PCMs focus on extant organisms, many methods can also be applied to extinct taxa and can incorporate information from the fossil record.
Phylogenetic nomenclature, often called cladistic nomenclature, is a method of nomenclature for taxa in biology that uses phylogenetic definitions for taxon names as explained below. This contrasts with the traditional approach, in which taxon names are defined by a type, which can be a specimen or a taxon of lower rank, and a description in words. Phylogenetic nomenclature is currently not regulated, but the International Code of Phylogenetic Nomenclature (PhyloCode) is intended to regulate it once it is ratified.
RedToL, or Red Algal Tree of Life, is part of the collaborative National Science Foundation Assembling the Tree of Life activity (AToL), funded through the Division of Environmental Biology, Directorate for Biological Sciences. The overall goal of AToL is to resolve evolutionary relationships for large groups of organisms throughout the history of life, with the research often involving large teams working across institutions and disciplines. Investigators are typically supported for projects in data acquisition, analysis, algorithm development and dissemination in computational phylogenetics and phyloinformatics.
TreeBASE is a repository of phylogenetic data published in scientific journals. In phylogenetic studies, research data are collected or generated, such as comparative observations made on a set of taxa, metadata about these taxa, and the phylogenetic trees that are inferred to best describe the evolutionary relationships between the taxa.
The following outline is provided as an overview of and topical guide to evolution:
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