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Lineage Sorting
Incomplete lineage sorting, also termed hemiplasy, deep coalescence, retention of ancestral polymorphism, or trans-species polymorphism, describes a phenomenon in population genetics when ancestral gene copies fail to coalesce (looking backwards in time) into a common ancestral copy until deeper than previous speciation events. It is caused by lineage sorting of genetic polymorphisms that were retained across successive nodes in the species tree. In other words, the tree produced by a single gene differs from the population or species level tree, producing a discordant tree. Whatever the mechanism, the result is that a generated species level tree may differ depending on the selected genes used for assessment. This is in contrast to complete lineage sorting, where the tree produced by the gene is the same as the population or species level tree. Both are common results in phylogenetic analysis, although it depends on the gene, organism, and sampling technique. Concept The conc ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Coalescent Theory
Coalescent theory is a model of how alleles sampled from a population may have originated from a common ancestor. In the simplest case, coalescent theory assumes no recombination, no natural selection, and no gene flow or population structure, meaning that each variant is equally likely to have been passed from one generation to the next. The model looks backward in time, merging alleles into a single ancestral copy according to a random process in coalescence events. Under this model, the expected time between successive coalescence events increases almost exponentially back in time (with wide variance). Variance in the model comes from both the random passing of alleles from one generation to the next, and the random occurrence of mutations in these alleles. The mathematical theory of the coalescent was developed independently by several groups in the early 1980s as a natural extension of classical population genetics theory and models, but can be primarily attributed to John ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Phylogeny
A phylogenetic tree (also phylogeny or evolutionary tree Felsenstein J. (2004). ''Inferring Phylogenies'' Sinauer Associates: Sunderland, MA.) is a branching diagram or a tree showing the evolutionary relationships among various biological species or other entities 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. In a ''rooted'' phylogenetic tree, each node with descendants represents the inferred most recent common ancestor of those descendants, and the edge lengths in some trees may be interpreted as time estimates. Each node is called a taxonomic unit. Internal nodes are generally called hypothetical taxonomic units, as they cannot be directly observed. Trees are useful in fields of biology such as bioinformatics, systematics, and phylogenetics. ''Unrooted'' trees illustrate only the relatedness of the leaf nodes and do not require the ancestral root to ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Lineage (evolution)
An evolutionary lineage is a temporal series of populations, organisms, cells, or genes connected by a continuous line of descent from ancestor to descendant.The Oxford English Dictionary defines biological lineage as "a sequence of species each of which is considered to have evolved from its predecessorOED definition of lineage/ref> Lineages are subsets of the evolutionary tree of life. Lineages are often determined by the techniques of molecular systematics. Phylogenetic representation of lineages 299x299px, A rooted tree of life into three ancient monophyletic lineages: bacteria, archaea, and eukaryotes">archaea.html" ;"title="bacteria, archaea">bacteria, archaea, and eukaryotes based on rRNA genes Lineages are typically visualized as subsets of a phylogenetic tree. A lineage is a single line of descent or linear chain within the tree, while a clade is a (usually branched) monophyletic group, containing a single ancestor and all its descendants. Phylogenetic trees are typic ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Multispecies Coalescent Process
Multispecies Coalescent Process is a stochastic process model that describes the genealogical relationships for a sample of DNA sequences taken from several species. It represents the application of coalescent theory to the case of multiple species. The multispecies coalescent results in cases where the relationships among species for an individual gene (the ''gene tree'') can differ from the broader history of the species (the ''species tree''). It has important implications for the theory and practice of phylogenetics and for understanding genome evolution. A ''gene tree'' is a binary graph that describes the evolutionary relationships between a sample of sequences for a non-recombining locus. A s''pecies tree'' describes the evolutionary relationships between a set of species, assuming tree-like evolution. However, several processes can lead to discordance between ''gene trees'' and ''species trees''. The Multispecies Coalescent model provides a framework for inferring species ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Laggar Falcon
The laggar falcon (''Falco jugger''), also known as the lugger falcon or jugger (from Hindi जग्गर — jaggar, “falcon”) is a mid-sized bird of prey which occurs in the Indian subcontinent from extreme southeastern Iran, southeastern Afghanistan, Pakistan, through India, Nepal, Bhutan, Bangladesh and northwestern Myanmar. It resembles the lanner falcon but is darker overall, and has blackish "trousers" ( tibiotarsus feathers). Fledglings have an almost entirely dark underside, and first-year subadult birds still retain much dark on the belly. This species belongs to a close-knit complex of falcons known as hierofalcons. In this group, there is ample evidence for rampant hybridization and incomplete lineage sorting which confounds analyses of DNA sequence data to a massive extent; molecular studies with small sample sizes can simply not be expected to yield reliable conclusions in the entire hierofalcon group. The radiation of the entire living diversity of hierofa ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Gibbon–human Last Common Ancestor
The phylogenetic split of the superfamily Hominoidea (apes) into the Hylobatidae (gibbons) and Hominidae (great apes) families (also dubbed "gibbon–human last common ancestor", GHLCA) is dated to the early Miocene, roughly . Hylobatidae has four gibbon genera ('' Hylobates'' with 9 species, ''Hoolock'' with 3 species, ''Nomascus'' with 7 species and ''Symphalangus'' with only 1 species) containing 20 different species. Hominidae has two subfamilies, Ponginae (orangutans) and Homininae (African apes, including the human lineage). Evolutionary history A 2014 whole-genome molecular dating analysis indicated that the gibbon lineage diverged from that of great apes (Hominidae) around 17 million years ago (), based on certain assumptions about the generation time and mutation rate. The extinct ''Bunopithecus sericus'' was a gibbon or gibbon-like ape. Adaptive divergence associated with chromosomal rearrangements led to rapid radiation of the four genera within the Hylobatida ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Historical Glottometry
Historical Glottometry is a method used in historical linguistics. It is a quantitative, non-cladistic approach to language subgrouping. The aim of Historical Glottometry (HG) is to address the limitations of the tree model when applied to dialect continua and linkages. It acknowledges that the genealogical structure of a linkage typically consists of entangled subgroups, and provides ways to reconstruct that internal structure by measuring the relative strength of these subgroups. This approach was developed by Alexandre François ( CNRS) and Siva Kalyan ( ANU). François (2014). François (2017). Kalyan & François (2018). While the method was initially applied to Oceanic languages, in recent years it has been applied to a much broader range of language families. Rationale Historical Glottometry grew out of the observation that a large number of language families in the world form linkages (a term coined by Malcolm Ross), i.e. they evolved out of former dialect continua in ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Alexandre François
Alexandre François is a French linguist specialising in the description and study of the indigenous languages of Melanesia. He belongs t''Lattice'' a research centre of the CNRS and École Normale Supérieure dedicated to linguistics. Research Language description and documentation François has done linguistic fieldwork in Vanuatu and the Solomon Islands. In 2002, he published a grammatical description of Araki, a language spoken by a handful of speakers on an islet south of Espiritu Santo (Vanuatu). Most of his research focuses on the northern islands of Vanuatu, known as the Torres and Banks Islands, an area where sixteen out of seventeen languages are still spoken: Hiw, Lo-Toga, Lehali, Löyöp, Mwotlap, Volow (extinct), Lemerig, Vera'a, Vurës, Mwesen, Mota, Nume, Dorig, Koro, Olrat, Lakon, Mwerlap - all descended from the Proto-Torres–Banks language, which was also reconstructed by him. After describing Mwotlap, the language with most speakers in that ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Linguistics
Linguistics is the science, scientific study of human language. It is called a scientific study because it entails a comprehensive, systematic, objective, and precise analysis of all aspects of language, particularly its nature and structure. Linguistics is concerned with both the Cognition, cognitive and social aspects of language. It is considered a scientific field as well as an academic discipline; it has been classified as a social science, natural science, cognitive science,Thagard, PaulCognitive Science, The Stanford Encyclopedia of Philosophy (Fall 2008 Edition), Edward N. Zalta (ed.). or part of the humanities. Traditional areas of linguistic analysis correspond to phenomena found in human linguistic systems, such as syntax (rules governing the structure of sentences); semantics (meaning); Morphology (linguistics), morphology (structure of words); phonetics (speech sounds and equivalent gestures in sign languages); phonology (the abstract sound system of a particular ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Criminal Transmission Of HIV
Criminal transmission of HIV is the intentional or reckless infection of a person with the human immunodeficiency virus (HIV). This is often conflated, in laws and in discussion, with criminal exposure to HIV, which does not require the transmission of the virus and often, as in the cases of spitting and biting, does not include a realistic means of transmission. Some countries or jurisdictions, including some areas of the U.S., have enacted laws expressly to criminalize HIV transmission or exposure, charging those accused with criminal transmission of HIV. Other countries charge the accused under existing laws with such crimes as murder, manslaughter, attempted murder, assault or fraud. Criminal transmission of HIV is now better known as HIV non-disclosure, which is the criminal offence in some jurisdictions for not disclosing an HIV positive status. This can be intentionally or unknowingly not disclosing HIV status and then exposing or transmitting HIV to a person. HIV non-di ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Population Bottleneck
A population bottleneck or genetic bottleneck is a sharp reduction in the size of a population due to environmental events such as famines, earthquakes, floods, fires, disease, and droughts; or human activities such as specicide, widespread violence or intentional culling, and human population planning. Such events can reduce the variation in the gene pool of a population; thereafter, a smaller population, with a smaller genetic diversity, remains to pass on genes to future generations of offspring through sexual reproduction. Genetic diversity remains lower, increasing only when gene flow from another population occurs or very slowly increasing with time as random mutations occur. This results in a reduction in the robustness of the population and in its ability to adapt to and survive selecting environmental changes, such as climate change or a shift in available resources. Alternatively, if survivors of the bottleneck are the individuals with the greatest genetic fitness, the ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Viral Phylodynamics
Viral phylodynamics is defined as the study of how epidemiological, immunological, and evolutionary processes act and potentially interact to shape viral phylogenies. Since the coining of the term in 2004, research on viral phylodynamics has focused on transmission dynamics in an effort to shed light on how these dynamics impact viral genetic variation. Transmission dynamics can be considered at the level of cells within an infected host, individual hosts within a population, or entire populations of hosts. Many viruses, especially RNA viruses, rapidly accumulate genetic variation because of short generation times and high mutation rates. Patterns of viral genetic variation are therefore heavily influenced by how quickly transmission occurs and by which entities transmit to one another. Patterns of viral genetic variation will also be affected by selection acting on viral phenotypes. Although viruses can differ with respect to many phenotypes, phylodynamic studies have to date ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
