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Retrotransposon Marker
Retrotransposon markers are components of DNA which are used as cladistic markers. They assist in determining the common ancestry, or not, of related taxa. The "presence" of a given retrotransposon in related taxa suggests their orthologous integration, a derived condition acquired via a common ancestry, while the "absence" of particular elements indicates the plesiomorphic condition prior to integration in more distant taxa. The use of presence/absence analyses to reconstruct the systematic biology of mammals depends on the availability of retrotransposons that were actively integrating before the divergence of a particular species. Details The analysis of SINEs – Short INterspersed Elements – LINEs – Long INterspersed Elements – or truncated LTRs – Long Terminal Repeats – as molecular cladistic markers represents a particularly interesting complement to DNA sequence and morphological data. The reason for this is that retrotransposons are assumed to represent powerf ...
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Cladistics
Cladistics (; ) is an approach to biological classification in which organisms are categorized in groups (" clades") based on hypotheses of most recent common ancestry. The evidence for hypothesized relationships is typically shared derived characteristics ( synapomorphies'')'' that are not present in more distant groups and ancestors. However, from an empirical perspective, common ancestors are inferences based on a cladistic hypothesis of relationships of taxa whose character states can be observed. Theoretically, a last common ancestor and all its descendants constitute a (minimal) clade. Importantly, all descendants stay in their overarching ancestral clade. For example, if the terms ''worms'' or ''fishes'' were used within a ''strict'' cladistic framework, these terms would include humans. Many of these terms are normally used paraphyletically, outside of cladistics, e.g. as a ' grade', which are fruitless to precisely delineate, especially when including extinct species. ...
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Ancestral
An ancestor, also known as a forefather, fore-elder or a forebear, is a parent or ( recursively) the parent of an antecedent (i.e., a grandparent, great-grandparent, great-great-grandparent and so forth). ''Ancestor'' is "any person from whom one is descended. In law, the person from whom an estate has been inherited." Two individuals have a genetic relationship if one is the ancestor of the other or if they share a common ancestor. In evolutionary theory, species which share an evolutionary ancestor are said to be of common descent. However, this concept of ancestry does not apply to some bacteria and other organisms capable of horizontal gene transfer. Some research suggests that the average person has twice as many female ancestors as male ancestors. This might have been due to the past prevalence of polygynous relations and female hypergamy. Assuming that all of an individual's ancestors are otherwise unrelated to each other, that individual has 2''n'' ancestors in the ...
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Mammalian
Mammals () are a group of vertebrate animals constituting the class Mammalia (), characterized by the presence of mammary glands which in females produce milk for feeding (nursing) their young, a neocortex (a region of the brain), fur or hair, and three middle ear bones. These characteristics distinguish them from reptiles (including birds) from which they diverged in the Carboniferous, over 300 million years ago. Around 6,400 extant species of mammals have been described divided into 29 orders. The largest orders, in terms of number of species, are the rodents, bats, and Eulipotyphla (hedgehogs, moles, shrews, and others). The next three are the Primates (including humans, apes, monkeys, and others), the Artiodactyla ( cetaceans and even-toed ungulates), and the Carnivora (cats, dogs, seals, and others). In terms of cladistics, which reflects evolutionary history, mammals are the only living members of the Synapsida (synapsids); this clade, together w ...
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Placental
Placental mammals (infraclass Placentalia ) are one of the three extant subdivisions of the class Mammalia, the other two being Monotremata and Marsupialia. Placentalia contains the vast majority of extant mammals, which are partly distinguished from monotremes and marsupials in that the fetus is carried in the uterus of its mother to a relatively late stage of development. The name is something of a misnomer considering that marsupials also nourish their fetuses via a placenta, though for a relatively briefer period, giving birth to less developed young which are then nurtured for a period inside the mother's pouch. Anatomical features Placental mammals are anatomically distinguished from other mammals by: * a sufficiently wide opening at the bottom of the pelvis to allow the birth of a large baby relative to the size of the mother. * the absence of epipubic bones extending forward from the pelvis, which are found in all other mammals. (Their function in non-placental mammals ...
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PLOS Biology
''PLOS Biology'' is a monthly peer-reviewed scientific journal covering all aspects of biology. Publication began on October 13, 2003. It is the first journal published by the Public Library of Science. The editor-in-chief is Nonia Pariente. In addition to research articles, the journal publishes magazine content aimed to be accessible to a broad audience. Article types in this section are essays, "unsolved mysteries", editorials, and synopses. Abstracting and indexing The journal is abstracted and indexed in: *Biological Abstracts *BIOSIS Previews *''Current Contents''/Agriculture, Biology & Environmental Sciences *''Current Contents''/Life Sciences *Chemical Abstracts Service * Embase *''Index Medicus''/MEDLINE/PubMed *Science Citation Index *Scopus *''The Zoological Record'' According to ''Journal Citation Reports'', the journal had a 2019 impact factor of 7.076. The journal does not list this impact factor on its website. Instead, the journal promotes the use of article level ...
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Marsupial
Marsupials are any members of the mammalian infraclass Marsupialia. All extant marsupials are endemic to Australasia, Wallacea and the Americas. A distinctive characteristic common to most of these species is that the young are carried in a pouch. Marsupials include opossums, Tasmanian devils, kangaroos, koalas, wombats, wallabies, bandicoots, and the extinct thylacine. Marsupials represent the clade originating from the last common ancestor of extant metatherians, the group containing all mammals more closely related to marsupials than to placentals. They give birth to relatively undeveloped young that often reside in a pouch located on their mothers' abdomen for a certain amount of time. Close to 70% of the 334 extant species occur on the Australian continent (the mainland, Tasmania, New Guinea and nearby islands). The remaining 30% are found in the Americas—primarily in South America, thirteen in Central America, and one species, the Virginia opossum, in Nort ...
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Strepsirrhine
Strepsirrhini or Strepsirhini (; ) is a suborder of primates that includes the lemuriform primates, which consist of the lemurs of Madagascar, galagos ("bushbabies") and pottos from Africa, and the lorises from India and southeast Asia. Collectively they are referred to as strepsirrhines. Also belonging to the suborder are the extinct adapiform primates which thrived during the Eocene in Europe, North America, and Asia, but disappeared from most of the Northern Hemisphere as the climate cooled. Adapiforms are sometimes referred to as being "lemur-like", although the diversity of both lemurs and adapiforms does not support this comparison. Strepsirrhines are defined by their "wet" (moist) rhinarium (the tip of the snout) – hence the colloquial but inaccurate term "wet-nosed" – similar to the rhinaria of canines and felines. They also have a smaller brain than comparably sized simians, large olfactory lobes for smell, a vomeronasal organ to detect pheromones, and a bicornua ...
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Hominoid
Apes (collectively Hominoidea ) are a clade of Old World simians native to sub-Saharan Africa and Southeast Asia (though they were more widespread in Africa, most of Asia, and as well as Europe in prehistory), which together with its sister group Cercopithecidae form the catarrhine clade, cladistically making them monkeys (though this is the subject of much debate). Apes do not have tails due to a mutation of the TBXT gene. In traditional and non-scientific use, the term "ape" can include tailless primates taxonomically considered Cercopithecidae (such as the Barbary ape and black ape), and is thus not equivalent to the scientific taxon Hominoidea. There are two extant branches of the superfamily Hominoidea: the gibbons, or lesser apes; and the hominids, or great apes. * The family Hylobatidae, the lesser apes, include four genera and a total of 20 species of gibbon, including the lar gibbon and the siamang, all native to Asia. They are highly arboreal and bipedal on the ...
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Cetartiodactyla
The even-toed ungulates (Artiodactyla , ) are ungulates—hoofed animals—which bear weight equally on two (an even number) of their five toes: the third and fourth. The other three toes are either present, absent, vestigial, or pointing posteriorly. By contrast, odd-toed ungulates bear weight on an odd number of the five toes. Another difference between the two is that many other even-toed ungulates (with the exception of Suina) digest plant cellulose in one or more stomach chambers rather than in their intestine as the odd-toed ungulates do. Cetaceans ( whales, dolphins, and porpoises) evolved from even-toed ungulates, and are therefore often classified under the same taxonomic branch because a species cannot outgrow its evolutionary ancestry; some modern taxonomists combine the two under the name Cetartiodactyla , while others opt to include cetaceans in the already-existing Artiodactyla. The roughly 270 land-based even-toed ungulate species include pigs, peccaries, hipp ...
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Whales
Whales are a widely distributed and diverse group of fully aquatic placental marine mammals. As an informal and colloquial grouping, they correspond to large members of the infraorder Cetacea, i.e. all cetaceans apart from dolphins and porpoises. Dolphins and porpoises may be considered whales from a formal, cladistic perspective. Whales, dolphins and porpoises belong to the order Cetartiodactyla, which consists of even-toed ungulates. Their closest non-cetacean living relatives are the hippopotamuses, from which they and other cetaceans diverged about 54 million years ago. The two parvorders of whales, baleen whales (Mysticeti) and toothed whales (Odontoceti), are thought to have had their last common ancestor around 34 million years ago. Mysticetes include four extant (living) families: Balaenopteridae (the rorquals), Balaenidae (right whales), Cetotheriidae (the pygmy right whale), and Eschrichtiidae (the grey whale). Odontocetes include the Monodontidae (b ...
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Phylogenetic
In biology, phylogenetics (; from Greek φυλή/ φῦλον [] "tribe, clan, race", and wikt:γενετικός, γενετικός [] "origin, source, birth") is the study of the evolutionary history and relationships among or within groups of organisms. These relationships are determined by Computational phylogenetics, phylogenetic inference methods that focus on observed heritable traits, such as DNA sequences, protein amino acid sequences, or morphology. The result of such an analysis is a phylogenetic tree—a diagram containing a hypothesis of relationships that reflects the evolutionary history of a group of organisms. The tips of a phylogenetic tree can be living taxa or fossils, and represent the "end" or the present time in an evolutionary lineage. A phylogenetic diagram can be rooted or unrooted. A rooted tree diagram indicates the hypothetical common ancestor of the tree. An unrooted tree diagram (a network) makes no assumption about the ancestral line, and does ...
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Homoplasy
Homoplasy, in biology and phylogenetics, is the term used to describe a feature that has been gained or lost independently in separate lineages over the course of evolution. This is different from homology, which is the term used to characterize the similarity of features that can be parsimoniously explained by common ancestry. Homoplasy can arise from both similar selection pressures acting on adapting species, and the effects of genetic drift. Most often, homoplasy is viewed as a similarity in morphological characters. However, homoplasy may also appear in other character types, such as similarity in the genetic sequence, life cycle types or even behavioral traits. Etymology The term homoplasy was first used by Ray Lankester in 1870. The corresponding adjective is either ''homoplasic'' or ''homoplastic''. It is derived from the two Ancient Greek words (), meaning "similar, alike, the same", and (), meaning "to shape, to mold". Parallelism and convergence Parallel and ...
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