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.
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While returning, the molecule becomes coalescent at certain point. This thin film of molecules act as normal shocks.
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Coalescent theory can be used to make inferences about population genetic parameters, such as migration, population size and recombination.
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Similar to the male differs as follows: Upperside: ground colour pale golden yellow; basal half of the wings suffused with dark olivaceous green; black markings as in the male but larger; on the forewing the spots of the subterminal series very large, coalescent or nearly coalescent with one another and with the dentate spots on the veins in the inner terminal line; the upper two spots also of the postdiscal series very large and coalescent, the upper of the two joining on above and below to the inner postdiscal lunate spot in interspace 6, thus enclosing a prominent lunule of the ground colour. Underside as in the male but paler.
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Both regular the coalescent and the shattered coalescent (which allows that multiple mutations may have occurred in the founding event, and that the disease may occasionally be triggered by environmental factors) have been put to work in understanding disease genes. Studies have been carried out correlating disease occurrence in fraternal and identical twins, and the results of these studies can be used to inform coalescent modeling. Since identical twins share all of their genome, but fraternal twins only share half their genome, the difference in correlation between the identical and fraternal twins can be used to work out if a disease is heritable, and if so how strongly.
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The probability density of the gene trees under the multispecies coalescent model is discussed along with its use for parameter estimation using multi-locus sequence data.
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Coalescents can be visualised using dendrograms which show the relationship of branches of the population to each other. The point where two branches meet indicates a coalescent event.
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Fixation rates can easily be modeled as well to see how long it takes for a gene to become fixed with varying population sizes and generations. For example, at The Biology Project Genetic Drift Simulation you can model genetic drift and see how quickly the gene for worm color goes to fixation in terms of generations for different population sizes. Additionally, fixation rates can be modeled using coalescent trees. A coalescent tree traces the descent of alleles of a gene in a population.
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Because of this, there is a strong chance that another Initial Coalescent group or several groups in the region attacked the Crow Creek village for its arable land and resources.(Zimmerman and Bradley 1993).
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Leaves 4–20 cm long; leaflets 5–6–paired. Peduncles very short, 2–3–flowered. Corolla whitetinged with lilac; carina darker. Flag 20–55 mm long; carina and alas coalescent with androphore up to ½ of length.
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Matthew Stephens (born 1970) is a Bayesian statistician and professor in the departments of Human Genetics and Statistics at the University of Chicago. He is known for the Li and Stephens model as an efficient coalescent.
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Coalescent is a science-fiction novel by Stephen Baxter. It is part one of the Destiny's Children series. The story is set in two main time periods: modern Britain, when George Poole finds that he has a previously unknown sister and follows a trail to a mysterious and ancient organisation in Rome (Puissant Order of Holy Mary Queen of Virgins); and the time of Regina, a girl growing up during the ending of Roman rule in Britain, around AD 400. Coalescent was nominated for the Arthur C. Clarke Award in 2004.
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He becomes obsessed with discovering the origin of this phenomenon, and his quest for answers drives a wedge between him and his family. Aunt Rosa Poole (from Coalescent), a Catholic priest and ex-member of the Order, helps Michael research the problem, drawing on her vast knowledge, stemming in small part from her relationship with the Coalescent hive and its historical archives. The rest of the Poole family joins the investigation when Morag appears during a trial test of the engineering project. This time, everyone sees Morag, even observing drones recording the event.
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Coalescent theory is a natural extension of the more classical population genetics concept of neutral evolution and is an approximation to the Fisher–Wright (or Wright–Fisher) model for large populations. It was discovered independently by several researchers in the 1980s.
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Frank T. Burbrink, Timothy J. Guiher (2014). Considering gene flow when using coalescent methods to delimit lineages of North American pitvipers of the genus Agkistrodon. Zoological Journal of the Linnean Society, December 2014. all of them monotypic and closely related.
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In a journal article entitled "The Crow Creek Massacre: Initial Coalescent Warfare and Speculations about the Genesis of Extended Coalescent", Zimmerman and Bradley propose that the severe conditions faced by the Crow Creek villagers were not short term. Based on the evidence of "active and organizing subperiostial hematomas along with the other bony alterations" found while examining remains, the villagers had long suffered malnutrition, in repeated episodes thought due to the unstable climate and drought reducing crops and food supplies.(Zimmerman and Bradley 1993:218). The presence of animal bones within the fortification ditch suggests that villagers ate their dogs because of hunger.
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Coalescent theory is a model of how gene variants 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).
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The utility of coalescent theory in the mapping of disease is slowly gaining more appreciation; although the application of the theory is still in its infancy, there are a number of researchers who are actively developing algorithms for the analysis of human genetic data that utilise coalescent theory. A considerable number of human diseases can be attributed to genetics, from simple Mendelian diseases like sickle-cell anemia and cystic fibrosis, to more complicated maladies like cancers and mental illnesses. The latter are polygenic diseases, controlled by multiple genes that may occur on different chromosomes, but diseases that are precipitated by a single abnormality are relatively simple to pinpoint and trace – although not so simple that this has been achieved for all diseases. It is immensely useful in understanding these diseases and their processes to know where they are located on chromosomes, and how they have been inherited through generations of a family, as can be accomplished through coalescent analysis.
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The species phylogeny is assumed to be known. Complete isolation after species divergence, with no migration, hybridization, or introgression is also assumed. We assume no recombination so that all the sites within the locus share the same gene tree (topology and coalescent times).
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1105 pp. . more. Agkistrodon laticinctus is a venomous pit viper species,Frank T. Burbrink, Timothy J. Guiher (2014). Considering gene flow when using coalescent methods to delimit lineages of North American pitvipers of the genus Agkistrodon. Zoological Journal of the Linnean Society, December 2014.
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Morris, A., Whittaker, J., & Balding, D. (2002). Fine-Scale Mapping of Disease Loci via Shattered Coalescent Modeling of Genealogies. The American Journal of Human Genetics, 70(3), 686–707. doi:10.1086/339271 Genetic diseases are passed from one generation to another just like other genes.
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This estimate is based on coalescent theory. Watterson's estimator is commonly used for its simplicity. When its assumptions are met, the estimator is unbiased and the variance of the estimator decreases with increasing sample size or recombination rate. However, the estimator can be biased by population structure.
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Eois nigriceps is a moth in the family Geometridae. It is found in Peru. The wingspan is about 30 mm. The forewings are wood-brown with dark grey lines, all swollen laterally on the costa into blackish coalescent blotches, so that the costal area appears dark.
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Flexion is predominantly suffixed and very regular, whereas the phonological processes are the most complex ones within the language. Stems often change their form while multiple-morpheme structures can become so coalescent that they are difficult to segment.Jendraschek, Gerd (2012) A Grammar of Iatmul. University of Regensburg, p. 21.
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Christina Anna Goldschmidt is a British probabilist known for her work in probability theory including coalescent theory, random minimum spanning trees, and the theory of random graphs. She is Professor of Probability in the Department of Statistics, University of Oxford and a Fellow of Lady Margaret Hall, Oxford.
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Mosaic retroposon insertion patterns in placental mammals. Genome Research 19: 868-75. Another analysis suggests that the root of this clade lies between the Atlantogenata and Boreoeutheria.Song S, Liu L, Edwards SV, Wu S (2012) Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model.
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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 Kingman. Advances in coalescent theory include recombination, selection, overlapping generations and virtually any arbitrarily complex evolutionary or demographic model in population genetic analysis. The model can be used to produce many theoretical genealogies, and then compare observed data to these simulations to test assumptions about the demographic history of a population.
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Hemidactylus eniangii is a species of forest gecko from the Dahomey Gap to western Cameroon.Wagner, Philipp, Adam D. Leaché, and Matthew K. Fujita. "Description of four new West African forest geckos of the Hemidactylus fasciatus Gray, 1842 complex, revealed by coalescent species delimitation." Bonn Zoological Bulletin 63.1 (2014): 1-14.
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The sutures are canaliculate. The six whorls are encircled by four coarsely tuberculose ribs on the upper surface ; the upper two contiguous, sometimes coalescent. The base of the shell shows 3 or 4 separated smaller beaded ribs, the broad interstices both above and below densely, finely spirally striate. The periphery is obtusely angular.
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The Bio.PopGen module adds support to Biopython for Genepop, a software package for statistical analysis of population genetics. This allows for analyses of Hardy–Weinberg equilibrium, linkage disequilibrium and other features of a population's allele frequencies. This module can also carry out population genetic simulations using coalescent theory with the fastsimcoal2 program.
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Goniobranchus bombayanus is a chromodorid nudibranch with a translucent white mantle with rounded purple spots and an orange submarginal band of coalescent spots. The centre of the back has a brownish hue and the surface is raised into tiny white papillae. The body reaches a length of 30 mm.Rudman, W.B., 2009 (Mar 9).
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70, no 2, 1er juin 2016, p. 145–152Toussaint, E.F., Morinière, J., Lam, A. and Turlin, B., 2016. Bayesian Poisson tree processes and multispecies coalescent models shed new light on the diversification of Nawab butterflies in the Solomon Islands (Nymphalidae, Charaxinae, Polyura). Zoological Journal of the Linnean Society, 178(2), pp.241-256.
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Both male and female have upperside black with orange markings. Forewing: discoidal streak broad, anteriorly twice indented, at apex extending into base of interspace 3; posterior discal spots coalescent, forming an irregular oblique short broad band; anterior spots also coalescent, oblique from costa; a postdiscal obscure grey incurved transverse line, and a very slender, also obscure, orange transverse subterminal line. Hindwing: a subbasal transverse broad band, and a much narrower postdiscal band curved inwards at the ends; beyond this the black terminal margin is traversed by a darker black subterminal line. Underside chestnut-brown, covered with short, slender, transverse brown striae on the margin of the orange markings, which are similar to those on the upperside but broader, paler, and less clearly defined.
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On the sides of the brown head there is a fine narrow dark stripe reaching the eyes.The Reptile DatabaseWagner, Philipp, Adam D. Leaché, and Matthew K. Fujita. "Description of four new West African forest geckos of the Hemidactylus fasciatus Gray, 1842 complex, revealed by coalescent species delimitation." Bonn Zoological Bulletin 63.1 (2014): 1-14.
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The Bioko leaf-toed gecko (Hemidactylus biokoensis) is a species of forest geckos from Bioko Island (Equatorial Guinea).Wagner, Philipp, Adam D. Leaché, and Matthew K. Fujita. "Description of four new West African forest geckos of the Hemidactylus fasciatus Gray, 1842 complex, revealed by coalescent species delimitation." Bonn Zoological Bulletin 63.1 (2014): 1-14.
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First, hybridization could have resulted in falcated duck mitochondrial DNA (mtDNA) introgressing into the gadwall gene pool. Second, gadwalls and falcated ducks could have diverged so recently that mtDNA lineages have not sorted to reciprocal monophyly. They used coalescent analyses of three independent loci to distinguish between these two hypotheses. Two lines of evidence support introgression.
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In genealogy and in phylogenetic studies of evolutionary biology, antecedents or antecessors are predecessors in a family line. For example, one is the descendant of their grandparents, who are one's antecedents. This term has particular utility in evolutionary coalescent theory, which models the process of genetic drift in reverse time. The antonym of antecedent is descendant.
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The Arzberger Site, designated by archaeologists with the Smithsonian trinomial 39HU6, is a major archaeological site in Hughes County, near Pierre, South Dakota. It was declared a National Historic Landmark in 1964. It is a large fortified village, that is the type site for the Initial Coalescent, a culture that flourished in the area c. 1200-1350 CE.
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Methods used to estimate the evolutionary divergence of taxa, including the multispecies coalescent process, suggest that most diversification of Melanohalea occurred throughout the Miocene (23.03 to 5.333 BP) and Pliocene (5.333 million to 2.58 BP), and divergence estimates suggest that diversification that occurred during the glacial cycles of the Pleistocene was not accompanied by speciation in Melanohalea.
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As all brachycephalids, Brachycephalus pombali are small: adult males measure and females in snout–vent length; this miniaturization is associated with loss of phalanges in hands and feet. The body is robust and toad-like. There is no tympanum. The general color is orange, lateral surfaces have small dark brown spots, and belly has brownish coalescent spots and small dots.
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Michael is returned to his own time, where he successfully completes the refrigeration project. The Kuiper anomaly, first introduced in Coalescent, disappears, and is revealed to be related to Alia's connection with Michael, having first appeared in the solar system at the time of Michael's birth. In the far future, the Transcendence collapses and the Witnessing program is shut down.
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Hindwing: a basal short, brownish-black, anteriorly attenuate bar placed obliquely, a transverse subbasal band of four large coalescent black spots, a transverse curved discal band twice broken as on the forewing and similar postdiscal subterminal and terminal markings. Antennae black, shafts ringed with white, head, thorax and abdomen dark brownish black; beneath: the palpi black, thorax and abdomen down the middle white.
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Sir Peter James Donnelly (born 15 May 1959) is an Australian mathematician and Professor of Statistical Science at the University of Oxford, and the CEO of Genomics PLC. He is a specialist in applied probability and has made contributions to coalescent theory. His research group at Oxford has an international reputation for the development of statistical methodology to analyze genetic data.
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His latest work concerns applications of coalescent theory to population genetics, particularly the mtDNA of whale lice, although members of his lab work on a variety of applied and theoretical topics that range from evolutionary ecology and genetics to mathematical biology and coalescent theory. In addition, he recently received an NSF grant to continue his work on the so-called "missing heritability" problem. His whale lice work had already shown that a genome should have many weakly deleterious mutations of small effect taken on their own but potentially large effect when taken together. This implies that the "missing" genes sought by, for example, human geneticists aren't actually missing: there are simply a lot more genes have a very small effect on fitness by themselves but have can have a large effect when the effects are combined.
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The type 1 and type 2 gene trees are both congruent with the species tree. The other two gene trees differ from the species tree; the two discordant gene trees are also deep coalescence trees. The distribution of times to coalescence is actually continuous for all of these trees. In other words, the exact coalescent time for any two loci with the same gene tree may differ.
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Late Triassic (220 Ma) The formation comprises arenites with a few thin clayey inter-beds. The sands overlie micro- conglomeratic bodies up to thick. Two-dimensional ripple marks (with wavelengths of nearly ), larger ripples (wavelengths of ), interference ripples, and mud cracks were recognized. The arenitic beds are also characterized by internal structures such as accretionary laminae, coalescent bodies, low-angle lamination, and cross stratification.
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Mount Meager is a mountain in the Pacific Ranges of the Coast Mountains in British Columbia, Canada. It represents the second highest peak of the Mount Meager massif, a group of coalescent stratovolcanoes in the Garibaldi Volcanic Belt. The mountain was the source of the 2010 Mount Meager landslide. On August 6, the southern peak of Meager collapsed in a series of major rockfalls.
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Their main aims are to characterize the risk of malignancy of nodules to better select nodules to submit to fine-needle aspiration cytology. Another imaging modality, which is ultrasound elastography, is also useful in diagnosing thyroid malignancy especially for follicular thyroid cancer. However, it is limited by the presence of adequate amount of normal tissue around the lesion, calcified shell around a nodule, cystic nodules, coalescent nodules.
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There was no professor of > statistics, the only chair having been abolished some years > before...[Maurice Bartlett and] I conspired to persuade Oxford to take > statistics seriously. During his time at Oxford, as well as holding a Fellowship at St Anne's College from 1978 to 1985, Kingman also chaired the Science and Engineering Research Council (now the Engineering and Physical Sciences Research Council (EPSRC)) from 1981 to 1985, was vice-president of the Institute of Statisticians from 1978 until 1992 and held visiting appointments at the University of Western Australia (1974) and the Australian National University (1978). It was also during this time that Kingman developed the theory of the Coalescent or Coalescent theory , a backwards-in-time theory of individuals in historical populations that, because it greatly simplifies computation, underlies much of modern population genomics . From October 1985, Kingman was elected Vice-Chancellor of the University of Bristol.
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A gene tree is a binary graph that describes the evolutionary relationships between a sample of sequences for a non- recombining locus. A species 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 phylogenies while accounting for ancestral polymorphism and gene tree-species tree conflict.
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Emperor Charlemagne, by Albrecht Dürer, 1511–1513, Germanisches Nationalmuseum. A royal descent is a genealogical line of descent from a past or present monarch. Both geneticists and genealogists have attempted to estimate the percentage of living people with royal descent. From a genetic perspective, the number of unprovable descendants must be virtually unlimited if going back enough generations, according to coalescent theory, as the possibility increases exponentially following every century back in time.
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Forewing: terminal two-thirds rich ochraceous brown, the green of the basal area bordered by black; discal and postdiscal bands also black, widened and diffusely coalescent posteriorly; an incomplete, very slender subterminal black line and broader black terminal edging, neither of which reaches to the apex. Hindwing much as on the upperside, but the yellow marking broader. Antennae dark red; head, thorax and abdomen black, covered somewhat densely with green hairs and scales.
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Michael consults members of the Poole family, who come together to work on the problem. Tom, John, and the elderly George (a principal character of Coalescent) reunite, and a maverick geoengineering company funds the project. Michael designs a subsurface refrigeration system that could stabilise the frozen hydrates. Meanwhile, Michael continues to be haunted by visions of his dead wife, apparitions he has been seeing his entire life, even before he first met her.
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In population genetics an idealised population is one that can be described using a number of simplifying assumptions. Models of idealised populations are either used to make a general point, or they are fit to data on real populations for which the assumptions may not hold true. For example, coalescent theory is used to fit data to models of idealised populations.. Nielsen, Rasmus, and Montgomery Slatkin. An Introduction to Population Genetics: Theory and Applications.
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In Drosophila populations of census size 16, the variance effective population size has been measured as equal to 11.5. This measurement was achieved through studying changes in the frequency of a neutral allele from one generation to another in over 100 replicate populations. For coalescent effective population sizes, a survey of publications on 102 mostly wildlife animal and plant species yielded 192 Ne/N ratios. Seven different estimation methods were used in the surveyed studies.
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For a long time PHASE was the most accurate method. PHASE was the first method to utilize ideas from coalescent theory concerning the joint distribution of haplotypes. This method used a Gibbs sampling approach in which each individuals haplotypes were updated conditional upon the current estimates of haplotypes from all other samples. Approximations to the distribution of a haplotype conditional upon a set of other haplotypes were used for the conditional distributions of the Gibbs sampler.
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Hindwing with similar markings; cell with two streaks, the upper forked towards apex; costa white, two spots not touching the vein below in interspace 8; paired spots on veins 5, 8, and 7 not coalescent but one behind the other, black. Underside similar. Antennae black; head and thorax streaked and spotted with black; abdomen white, with broad dusky black streak above. Chrysalis A variety kanarensis, Moore, has been noted to be identical in markings but always smaller.
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Such inference is analytically intractable for many demographic models, but the authors presented ways of simulating coalescent trees under the putative models. A sample from the posterior of model parameters was obtained by accepting/rejecting proposals based on comparing the number of segregating sites in the synthetic and real data. This work was followed by an applied study on modeling the variation in human Y chromosome by Jonathan K. Pritchard et al. using the ABC method.
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Measured coalescent effective population sizes vary between genes in the same population, being low in genome areas of low recombination and high in genome areas of high recombination. Sojourn times are proportional to N in neutral theory, but for alleles under selection, sojourn times are proportional to log(N). Genetic hitchhiking can cause neutral mutations to have sojourn times proportional to log(N): this may explain the relationship between measured effective population size and the local recombination rate.
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Male upperside dead white. Forewing: a narrow band of irrorated black scales along basal portion of costa; a wedge-shaped short costal black spot before the apex; apex black; that colour continued along the anterior portion of the termen as a series of inwardly-pointed triangular coalescent spots at apices of veins 4 and 5; lastly, a large black spot in the outer half of interspace 3. Hindwing: a black costal spot just before the apex, otherwise uniform white. Underside: ground colour similar.
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Thus it can be beneficial to CST analysis to compare the same pathogens occurring in different host species. Phylogenetic analysis can be used to track a pathogens history through different species populations. Even if a pathogen is new and highly divergent, phylogenetic comparison can be very insightful. A useful strategy for investigating the history of epidemics caused by pathogen transmission combines molecular clock analysis, to estimate the timescale of the epidemic, and coalescent theory, to infer the demographic history of the pathogen.
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The forewings are chocolate brown, with yellow nervures and a large yellow patch in the basal one-third of the wing below the cell. There is a postmedian band of intranervular coalescent golden-yellow patches, the upper four wedge shaped, the lower four arrowhead shaped, the points of all truncated. The hindwings are the same ground colour, but with only six patches in the postmedian band, all of which are arrowhead shaped, the lower three only having their points truncated.
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The hindwings are much paler and almost patternless and the transverse band of the forewings is also more concavely curved. Females have liver-chestnut forewings with a white spot below the median in the basal one-third of the wing, a median slightly sinuate darker band and the nervures and marginal line are yellow. There is a postdiscal coalescent band of intranervular white wedge-shaped patches truncated distad. The hindwings are similar in ground colour, but the band of white patches is lunate.
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These two are closely linked, and derived from F-statistics, but they are not identical. Today, the effective population size is usually estimated empirically with respect to the sojourn or coalescence time, estimated as the within-species genetic diversity divided by the mutation rate, yielding a coalescent effective population size. Another important effective population size is the selection effective population size 1/scritical, where scritical is the critical value of the selection coefficient at which selection becomes more important than genetic drift.
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According to the neutral theory of molecular evolution, a neutral allele remains in a population for Ne generations, where Ne is the effective population size. An idealised diploid population will have a pairwise nucleotide diversity equal to 4\muNe, where \mu is the mutation rate. The sojourn effective population size can therefore be estimated empirically by dividing the nucleotide diversity by the mutation rate. The coalescent effective size may have little relationship to the number of individuals physically present in a population.
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The extent of this excess can be quantified as the inbreeding coefficient, F. Individuals can be clustered into K subpopulations. The degree of population structure can then be calculated using FST, which is a measure of the proportion of genetic variance that can be explained by population structure. Genetic population structure can then be related to geographic structure, and genetic admixture can be detected. Coalescent theory relates genetic diversity in a sample to demographic history of the population from which it was taken.
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Triaenops menamena is currently one of four living species in the genus Triaenops; a 2009 revision by Petr Benda and Peter Vallo split off the African T. afer and the Yemeni T. parvus from T. persicus and removed three other species, including two from Madagascar, to the separate genus Paratriaenops.Benda and Vallo, 2009, p. 34 An extinct species, Triaenops goodmani, is known from northwestern Madagascar. In 2007 and 2008, Amy Russell and colleagues used phylogenetic and coalescent methodologies to investigate the history of the Triaenops group.
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Dawkins fails to explicitly contrast ancestor organism and descendant organisms against ancestor genes and descendant genes in this chapter. But the first half of the chapter is really about differences between these two models of lineage. While organisms have ancestry graphs and progeny graphs via sexual reproduction, a gene has a single chain of ancestors and a tree of descendants. Given any gene in the body of an organism, we can trace a single chain of ancestor organisms back in time, following the lineage of this one gene, as stated in the coalescent theory.
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The "Jean-Baptiste Lainé" or Mantle site in the town of Whitchurch–Stouffville, north-east of Toronto, is the largest and most complex ancestral Wendat-Huron village to be excavated in the Lower Great Lakes region to date.Toronto Museum Project, Dunsmere Pipe . An exhaustive archaeological study of the Mantle Site is provided by Jennifer Birch, " Coalescent Communities in Iroquoian Ontario," unpublished PhD Thesis, McMaster University, Hamilton, 2010. Formerly thought to have been active 1500-1530, the prime period of the site has been shifted to 1587-1623, based on radiocarbon dating and Bayesian analysis.
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Denisovans appear to have crossed the Wallace Line. Though their remains have been identified in only two locations, traces of Denisovan DNA in modern humans suggest they ranged across East Asia, and potentially western Eurasia. In 2019, geneticist Guy Jacobs identified three distinct populations of Denisovans in, respectively, Siberia and East Asia, New Guinea and nearby islands, and Oceania and to a lesser extent across Asia. Using coalescent modeling, the Denisova Cave Denisovans split from the second population about 283,000 years ago; and from the third population about 363,000 years ago.
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The forewings are greyish-cream-white suffused and freckled with cinnamon grey. There is a darker outwardly curved subbasal band and a sharply angled antemedian band just touching a vitreous patch, beyond this patch are three rather indistinct bands of darker coalescent lunate marks. The transverse band from the apex to the inner margin is much more basad and much more defined, also straighter and the submarginal cloud band is much fainter. The hindwings are similar, but only with one antemedian band and a brown and straight postmedian band.
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Its prostomium is wider than long, with 4 coalescent lensed eyes arranged trapezoidally; anterior eyespots are absent. It counts with pyriform antennae with bulbous bases and elongated tips, its median antenna measuring 40 µm long, while lateral ones measure 33 µm, which is longer than its prostomium and palps together. Its median antenna is inserted between its anterior pair of eyes, the lateral ones attached on the anterior margin of its prostomium. The animal's palps are ventrally-directed, fused along their length and with a dorsal notch and few small papillae.
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When performing a statistical test such as Tajima's D, the critical question is whether the value calculated for the statistic is unexpected under a null process. For Tajima's D, the magnitude of the statistic is expected to increase the more the data deviates from a pattern expected under a population evolving according to the standard coalescent model. Tajima (1989) found an empirical similarity between the distribution of the test statistic and a beta distribution with mean zero and variance one. He estimated theta by taking Watterson's estimator and dividing it by the number of samples.
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The Arzberger Site is located on a terrace overlooking the east bank of the Missouri River, about southeast of Pierre. The site is that of a fortified village, which originally had a wooden stockade encircling an area of about . The stockade was fortified with 24 bastions, and there were 44 house structures inside it. Although the site is considered the type site for the Initial Coalescent, it appears temporally late in the sequence of sites now associated with that cultural phase, and may be one of its final outposts.
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If phylogenetic signal of an alignment is too low then a longer alignment or an alignment of another gene in the organism may be necessary to perform phylogenetic analysis. Typically substitution saturation is only in issue in data sets with viral sequences. Most algorithms used for phylogenetic analysis do not take into recombination into account, which can alter the molecular clock and coalescent estimates of a multiple sequence alignment. Strains that show signs of recombination should either be excluded from the data set or analyzed on their own.
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The Crow Creek site, designated 39BF11 under the Smithsonian site numbering system, is located along the Missouri River in central South Dakota. The site is located on lands now under the control of the US Army Corps of Engineers due to its flood control and other projects on the river. It is surrounded by the territory of the Crow Creek Indian Reservation. The descendants of the people of the Middle Missouri and Central Plains/Initial Coalescent cultures now live in North Dakota as the Mandan and Arikara nations, respectively, of the Three Affiliated Tribes (together with the Hidatsa).
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The joint distribution of f(T_i,t_i\mid\Theta) is derived directly in this section. Two sequences from different species can coalesce only in one populations that are ancestral to the two species. For example, sequences H and G can coalesce in populations HCG or HCGO, but not in populations H or HC. The coalescent processes in different populations are different. For each population, the genealogy is traced backward in time, until the end of the population at time \tau , and the number of lineages (m) entering the population and the number of lineages leaving it (n) are recorded.
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The local density of Single Nucleotide Polymorphisms (SNPs) within the human genome, as well as that of genes, appears to cluster in accord with the variance-to-mean power law and the Tweedie compound Poisson–gamma distribution. In the case of SNPs their observed density reflects the assessment techniques, the availability of genomic sequences for analysis, and the nucleotide heterozygosity. The first two factors reflect ascertainment errors inherent to the collection methods, the latter factor reflects an intrinsic property of the genome. In the coalescent model of population genetics each genetic locus has its own unique history.
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Consider a single gene locus sampled from two haploid individuals in a population. The ancestry of this sample is traced backwards in time to the point where these two lineages coalesce in their most recent common ancestor (MRCA). Coalescent theory seeks to estimate the expectation of this time period and its variance. The probability that two lineages coalesce in the immediately preceding generation is the probability that they share a parental DNA sequence. In a population with a constant effective population size with 2Ne copies of each locus, there are 2Ne "potential parents" in the previous generation.
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It is also possible to consider the ancestry of individual genes (or groups of genes, haplotypes) instead of an organism as a whole. Coalescent theory describes a stochastic model of how the ancestry of such genetic markers maps to the history of a population. Unlike organisms, a gene is passed down from a generation of organisms to the next generation either as perfect replicas of itself or as slightly mutated descendant genes. While organisms have ancestry graphs and progeny graphs via sexual reproduction, a gene has a single chain of ancestors and a tree of descendants.
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Mount Meager, located north of Vancouver, is a peak of the Mount Meager massif. This is a group of coalescent stratovolcanoes and the largest volcanic centre in the Garibaldi Volcanic Belt. It comprises about of eruptive rocks that were deposited during four distinct eruptive periods, the first beginning 2.2 million years ago. During the present period (beginning 150,000 years ago), it has erupted more than five times, producing ash falls, pyroclastic flows, lava flows and lahars. The only identified Holocene eruption was in about 410 BC and created a diverse sequence of volcanic deposits well exposed along the Lillooet River.
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When infinitesimal effects at a large number of gene loci are considered, together with the assumption of linkage equilibrium or quasi-linkage equilibrium, one derives quantitative genetics. Ronald Fisher made fundamental advances in statistics, such as analysis of variance, via his work on quantitative genetics. Another important branch of population genetics that led to the extensive development of coalescent theory is phylogenetics. Phylogenetics is an area that deals with the reconstruction and analysis of phylogenetic (evolutionary) trees and networks based on inherited characteristicsCharles Semple (2003), Phylogenetics, Oxford University Press, Traditional population genetic models deal with alleles and genotypes, and are frequently stochastic.
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However, as well as being an administrative tool, a series of censuses can act as a coalescent of the population or at least of parts of it, causing various groups within the whole to form identities in space and over time. The ability of people to classify themselves can both reinforce and create classifications with which they identify. While the above is true of all population censuses, the nature of society in British India posed particular problems. Even the geographically smaller post-Partition India contains a myriad of languages and cultures, ethnicities and religions, many of which have evolved over several millennia.
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Molstad Village, designated by the Smithsonian trinomial 39DW234, is an archaeological site in Dewey County, South Dakota, United States, near the city of Mobridge. It was declared a National Historic Landmark in 1964. The site contains the remains of a small fortified Native America village, consisting of earth lodges surrounded by a bastioned palisade, with further lodges scattered in the area outside the fortification. Evidence gathered at the site indicates it was occupied for a relatively brief period in the mid-1500s CE, and was assigned to the Chouteau aspect of Middle Missouri taxonomy, later known as the Extended Coalescent phase.
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The process is also called the Censored Coalescent. Discordance between gene trees and the species tree can lead to the cases where characters that appear to be homoplastic (to be gained or lost independently in separate lineages) given the relationships among species when those characters actually has a single origin; this phenomenon is called hemiplasy. Many studies that have focused on hemiplasy have focused on genomic characters like nucleotide or amino acid substitutions, indels, or karyotypic differences (though the last of these is thought to be less subject to hemiplasy than many other characters). However, phenotypic characters also have the potential to exhibit hemiplasy.
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The La Plata or Chusma Fault extends across the eastern slope of the Central Ranges of the Colombian Andes, southeast of the city of Neiva in southwestern Colombia. The fault displaces Triassic, Jurassic and Cretaceous sedimentary rocks, as well as Tertiary volcanic rocks. Coalescent Quaternary alluvial fan deposits are offset by the La Plata Fault. The trace is characterised by old retreated and declined scarps, en-echelon semiparallel associated faults that cut alluvial deposits of the Páez River and local lahar deposits, a well developed topographic fault-line expression, and a probable pull-apart basin filled with Quaternary alluvial fans and alluvium near the town of La Plata.
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At shorter time scales and finer geographical scales, HIV phylogenies may reflect epidemiological dynamics related to risk behavior and sexual networks. Very dense sampling of viral sequences within cities over short periods of time has given a detailed picture of HIV transmission patterns in modern epidemics. Sequencing of virus from newly diagnosed patients is now routine in many countries for surveillance of drug resistance mutations, which has yielded large databases of sequence data in those areas. There is evidence that HIV transmission within heterogeneous sexual networks leaves a trace in HIV phylogenies, in particular making phylogenies more imbalanced and concentrating coalescent events on a minority of lineages.
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Linkage mapping methods, including Coalescent theory can be put to work on these diseases, since they use family pedigrees to figure out which markers accompany a disease, and how it is inherited. At the very least, this method helps narrow down the portion, or portions, of the genome on which the deleterious mutations may occur. Complications in these approaches include epistatic effects, the polygenic nature of the mutations, and environmental factors. That said, genes whose effects are additive carry a fixed risk of developing the disease, and when they exist in a disease genotype, they can be used to predict risk and map the gene.
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Due to this, she suspects that the real Rocha may have been killed by this strange coalescent organism, and a replica of him may have attacked Aquiel in search of a new body. Believing that the organism now has Aquiel's body, Riker and Worf race to Aquiel's quarters and stop the ritual she is conducting with La Forge, believing she was about to attack him. Morag is also arrested, as it is just as likely he is the organism. With Aquiel and Morag in the brig, the Enterprise proceeds to the nearest starbase as the crew keep a close watch on them both - the organism may need a new body soon.
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The effective population size is most commonly measured with respect to the coalescence time. In an idealised diploid population with no selection at any locus, the expectation of the coalescence time in generations is equal to twice the census population size. The effective population size is measured as within-species genetic diversity divided by four times the mutation rate \mu, because in such an idealised population, the heterozygosity is equal to 4N\mu. In a population with selection at many loci and abundant linkage disequilibrium, the coalescent effective population size may not reflect the census population size at all, or may reflect its logarithm.
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Under conditions of genetic drift alone, every finite set of genes or alleles has a "coalescent point" at which all descendants converge to a single ancestor (i.e. they 'coalesce'). This fact can be used to derive the rate of gene fixation of a neutral allele (that is, one not under any form of selection) for a population of varying size (provided that it is finite and nonzero). Because the effect of natural selection is stipulated to be negligible, the probability at any given time that an allele will ultimately become fixed at its locus is simply its frequency p in the population at that time.
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Where the branch length in coalescent units (T) is also written in an alternative form: the number of generations (t) divided by twice the effective population size (Ne). Pamilo and Nei also derived the probability of congruence for rooted trees of four and five taxa as well as a general upper bound on the probability of congruence for larger trees. Rosenberg followed up with equations used for the complete set of topologies (although the large number of distinct phylogenetic trees that becomes possible as the number of taxa increases makes these equations impractical unless the number of taxa is very limited). The phenomenon of hemiplasy is a natural extension of the basic idea underlying gene tree-species tree discordance.
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An analysis based on morphology suggests that the four genera are ordered as (Symphalangus, (Nomascus, (Hoolock, Hylobates))) A coalescent-based species tree analysis of genome-scale datasets suggests a phylogeny for the four genera ordered as (Hylobates, (Nomascus, (Hoolock, Symphalangus))). At the species level, estimates from mitochondrial DNA genome analyses suggest that Hylobates pileatus diverged from H. lar and H. agilis around 3.9 Mya, and H. lar and H. agilis separated around 3.3 Mya. Whole genome analysis suggests divergence of Hylobates pileatus from Hylobates moloch 1.5-3.0 Mya. The extinct Bunopithecus sericus is a gibbon or gibbon- like ape which, until recently, was thought to be closely related to the hoolock gibbons.
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One drawback of performing a McDonald–Kreitman test is that the test is vulnerable to error, as with every other statistical test. Many factors can contribute to errors in estimates of the level of adaptive evolution, including presence of slightly deleterious mutations, variation of mutation rates across the genome, variation in coalescent histories across the genome, and changes in the effective population size. All these factors result in α being underestimated. However, according to research done by Charlesworth (2008), Andolfatto(2008), and Eyre-Walker(2006), none of these factors are significant enough to make scientists believe the McDonald–Kreitman test is unreliable, except for the presence of slightly deleterious mutations in species.
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Crandall received a Bachelor of Arts degree in mathematics and biology from Kalamazoo College in 1987. He received a Master of Arts degree in coalescent theory and network estimation of gene genealogies (statistics) from Washington University in St. Louis in 1992. He then proceeded to obtain a Doctor of Philosophy in biology and biomedical sciences from Washington University in St. Louis in 1993, for research supervised by Alan Templeton on the molecular systematics and evolutionary biology in the crayfish subgenus Procericambarus (Decapoda: Cambaridae). Crandall then held the Alfred P. Sloan and National Science Foundation Postdoctoral Fellowships at the University of Texas, studying molecular evolution under advisors Jim Bull and David Hillis, between 1993 and 1996.
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660x660px If we consider a rooted three-taxon tree, the simplest non-trivial phylogenetic tree, there are three different tree topologies but four possible gene trees. The existence of four distinct gene trees despite the smaller number of topologies reflects the fact that there are topologically identical gene tree that differ in their coalescent times. In the type 1 tree the alleles in species A and B coalesce after the speciation event that separated the A-B lineage from the C lineage. In the type 2 tree the alleles in species A and B coalesce before the speciation event that separated the A-B lineage from the C lineage (in other words, the type 2 tree is a deep coalescence tree).
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Costa broadly, termen decreasingly from apex to tornus dark brown; rest of the wing dark shining yellow, suffused for about two thirds from base with light brown that leaves a transverse broad post discal band of the yellow ground colour prominently apparent, the inner margin of the broad, dark brown, terminal edging vandyked. Hindwing: dark brown; a subterminal series of yellow, inwardly pointed, large, cone-shaped coalescent spots; the bases of the spots rest on an anteciliary brown line and bear each a dark brown spot that is very near to and in some specimens anteriorly touches the anteciliary line, the posterior two brown spots geminate. Cilia of both forewings and hindwings white alternated with fuscous. Underside, precisely similar to that of the male.
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The human single-nucleotide polymorphism (SNP) map has revealed large regional variations in heterozygosity, more so than can be explained on the basis of (Poisson-distributed) random chance. In part, these variations could be explained on the basis of assessment methods, the availability of genomic sequences, and possibly the standard coalescent population genetic model. Population genetic influences could have a major influence on this variation: some loci presumably would have comparatively recent common ancestors, others might have much older genealogies, and so the regional accumulation of SNPs over time could be quite different. The local density of SNPs along chromosomes appears to cluster in accordance with a variance to mean power law and to obey the Tweedie compound Poisson distribution.
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Most estimations of numbers were based on single migrating colonies, and it is unknown how many of these existed at a given time. American writer Christopher Cokinos has suggested that if the birds flew single file, they would have stretched around the earth 22 times. A 2014 genetic study (based on coalescent theory and on “sequences from most of the genome” of three individual passenger pigeons) suggested that the passenger pigeon population experienced dramatic fluctuations across the last million years, due to their dependence on availability of mast (which itself fluctuates). The study suggested the bird was not always abundant, mainly persisting at around 1/10,000 the amount of the several billions estimated in the 1800s, with vastly larger numbers present during outbreak phases.
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Hindwing: an obliquely placed basal streak, a row of three spots across the cell, the upper two spots much elongated, a short bar on the discocellulars and an elongate, transverse, subcostal spot above it; four discal spots, the upper four placed obliquely two and two, the lower two transverse, coalescent; postdiscal band, subterminal transverse series of spots and anteciliary line as on the forewing; the postdiscal band lunular, all or some of the spots of the subterminal series with shining bluish metallic scales. Cilia as on the upperside; tail black tipped with white. Antenna, head, thorax and abdomen black, the shafts of the antennae ringed with white, the thorax with a little bluish pubescence; beneath: the palpi, thorax and abdomen white.
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Male upperside: brown, in fresh specimens generally uniform, in some slightly paler along a posterior area from base outwards on the forewing. This is more commune in the female than in the male. Underside: milk white. Forewing: a few very obscure specks along the costa, and a postdiscal transverse series of four transversely elongate spots, or short broad lines, pale brown; the spots of the latter arranged two subcostal and two posterior close to the tornal angle; beyond these is a continuous transverse broad brown line that gets paler posteriorly, from costa to dorsum, followed by a subterminal series of similarly-coloured transverse spots, one in each interspace; at the apex these are generally coalescent with the inner brown line; lastly an anteciliary dark brown line.
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The multispecies coalescent has profound implications for the theory and practice of molecular phylogenetics. Since individual gene trees can differ from the species tree one cannot estimate the tree for a single locus and assume that the gene tree correspond the species tree. In fact, one can be virtually certain that any individual gene tree will differ from the species tree for at least some relationships when any reasonable number of taxa are considered. However, gene tree-species tree discordance has an impact on the theory and practice of species tree estimation that goes beyond the simple observation that one cannot use a single gene tree to estimate the species tree because there is a part of parameter space where the most frequent gene tree is incongruent with the species tree.
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This is mathematically convenient, as the standard exponential distribution has both the expected value and the standard deviation equal to 2Ne. Therefore, although the expected time to coalescence is 2Ne, actual coalescence times have a wide range of variation. Note that coalescent time is the number of preceding generations where the coalescence took place and not calendar time, though an estimation of the latter can be made multiplying 2Ne with the average time between generations. The above calculations apply equally to a diploid population of effective size Ne (in other words, for a non-recombining segment of DNA, each chromosome can be treated as equivalent to an independent haploid individual; in the absence of inbreeding, sister chromosomes in a single individual are no more closely related than two chromosomes randomly sampled from the population).
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Simulations have shown that there are parts of species tree parameter space where maximum likelihood estimates of phylogeny are incorrect trees with increasing probability as the amount of data analyzed increases. This is important because the "concatenation approach," where multiple sequence alignments from different loci are concatenated to form a single large supermatrix alignment that is then used for maximum likelihood (or Bayesian MCMC) analysis, is both easy to implement and commonly used in empirical studies. This represents a case of model misspecification because the concatenation approach implicitly assumes that all gene trees have the same topology. Indeed, it has now been proven that analyses of data generated under the multispecies coalescent using maximum likelihood analysis of a concatenated data are not guaranteed to converge on the true species tree as the number of loci used for the analysis increases (i.e.
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Caterpillar left The Malabar tree nymph has a wingspan of 120–154 mm. It appears as a mostly white butterfly with black markings. Upperside semitransparent white, sometimes slightly infuscate with a powdering of black scales. Forewing with the following black marks: narrow margins on both sides of the veins, a dusky streak along dorsum, large sub-basal spots in interspaces 1 and 2 (produced inwardly in former), a large oval spot crossing three streaks in discoidal cell, a spot above it in interspace 11, a broad margin to the discocellulars and three rows of spots on outer half of wing, the discal series outwardly conical and curved sharply inwards opposite apex, the subterminal series in pairs coalescent on the veins, the terminal series elongate on veins and in interspaces; costa with a black streak at base, beyond black and white alternately.
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Closely resembles Tirumala limniace, Cramer, but is always sufficiently distinct to be easily recognized, even on the wing. From T. limniace it differs on the upperside in the ground colour being darker and the semihyaline markings narrower, more distinct, and of a bluer tint, In the forewing, in interspace 1 the two streaks are narrower, never coalescent, the upper one forming an oval detached spot; the short streaks above vein 5 are outwardly never truncate, always acute. In the hindwing the two streaks if the discoidal cell united at base are wide apart at their apices, the lower one never formed into a hook. On the underside this species is generally darker, the apex of the forewing and the whole of the ground colour of the hindwing not being of the conspicuous golden brown that they are in T. limniace.
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Wilson, Cann, and Stoneking measured differences among many individuals from different human continental groups, and found that humans from Africa showed the greatest inter-individual differences, consistent with an African origin of the human species (the Recent African origin of modern humans or "Out of Africa" hypothesis). The data further indicated that all living humans shared a common maternal ancestor, who lived in Africa only a few hundreds of thousands of years ago. This common ancestor became widely known in the media and popular culture as the Mitochondrial Eve. This had the unfortunate and erroneous implication that only a single female lived at that time, when in fact the occurrence of a coalescent ancestor is a necessary consequence of population genetic theory, and the Mitochondrial Eve would have been only one of many humans (male and female) alive at that time.
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Coalescent lesions may cover large portions of the body with extensive tissue destruction. Although some vaccinia viruses commonly disseminate through the bloodstream, the NYCBOH strain reportedly causes only limited viremia in a small percentage of recipients during the period of pustule formation Fenner F, Henderson DA, Arita I, Jezek Z, Ladnyi I. , Smallpox and its eradication, 1988GenevaWorld Health Organization Blattner RJ, Normal JO, Heys FM, Aksu I. Antibody response to cutaneous inoculation with vaccinia virus: viremia and viruria in vaccinated children, J Pediatr, 1964, vol. 64 (pg. 839-52). The inflammatory process reaches its peak by days 10–12 after vaccination and begins to resolve by day 14, with shedding of the scab and other pustules by day 21. This sequence of events, which simulates the development of a smallpox "pock" , is known as a “take” reaction.
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Hindwing: a transverse, discal, very irregular band widely interrupted in the middle; two coalescent spots beyond transversely across interspaces 4 and 5, followed by a subterminal, complete, curved series of distinct lunules that are edged slenderly on the outer side with white, and a prominent anteciliary white line. Cilia of both forewings and hindwings brown; filamentous short tail to latter black tipped with white. Antennae, head, thorax and abdomen black, the abdomen barred with white on the sides; beneath: the palpi, thorax and abdomen medially white. Female closely resembles the male, but on the upperside, the medial, broad, oblique white band that crosses the wings is distinctly broader and on the forewing extends farther towards the costa in a point, while on the hindwing there is in addition, in many specimens, a subterminal complete transverse series of linear white dots.
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Female from Mumbai, India Underside: a darker yellow, sparsely irrorated (sprinkled) with fusco-ferruginous short strigae and minute spots. Forewing: base and posterior area broadly, with a whitish pale virescent (greenish) tint; the strigae and minute spots most numerous towards the apex and along the termen; interspaces 4, 5, 6 and 8 with a curved sub-apical series of small, rounded, dull ferruginous spots and a similar spot on the discocellulars. Hindwing also with a ferruginous spot on the discocellulars, followed by a postdiscal series of similar spots in interspaces 3 to 8, all or most of them centred with white; the spots in interspaces 5, 6 and 8 the largest, those in 5 and 6 often coalescent. Antennae and thorax anteriorly dull ferruginous, thorax posteriorly and abdomen above fuscous black; head, thorax and abdomen beneath yellow.
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The wingspan is .Forewing pale dull rosy, with olive fuscous shading; a brown spot at middle of base: inner and outer lines nearly straight, edged with brown; median area from inner margin to above middle ferruginous brown; a small V-shaped spot on vein 2 and a small round spot close beyond it pale golden; reniform stigma in part brownish edged; subterminal line suffusedly margined with olive brown, except above anal angle; hindwing fuscous brown, the terminal border darker; in the rarer form percontationis Tr. the two golden marks are coalescent; on the other hand the outer spot, and sometimes both, may be wanting as in the ab. inscripta Esp.; in the form inscripta, from the Baltic provinces of Bussia, the ground colour is much darker, especially in the lower part of the median area; a similar dark form, but with the golden markings confluent as in percontationis Tr., — subsp.
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Stephanorhinus species are well known in Europe from the Late Pliocene through the Pleistocene, and China from the Pleistocene, with two species, Merck's rhinoceros and the narrow-nosed rhinoceros surviving into the last glacial period. Although some morphological studies questioned the relationship, recent molecular analysis has supported the close relationship. Pairwise sequential Markovian coalescent (PSMC) analysis of a complete nuclear genome of a Sumatran specimen suggested strong fluctuations in population size, with a general trend of decline over the course of the Middle to Late Pleistocene with an estimated peak effective population size of 57,800 individuals 950,000 years ago, declining to around 500–1,300 individuals at the start of the Holocene, with a slight rebound during the Eemian Interglacial. This was likely due to climate change causing limiting suitable habitat for the Rhinoceros, causing severe population fluctuations as well as population fragmentation due to the flooding of Sundaland.
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Malaya Wet-season brood. male. Upperside: violaceous blue, with brilliant iridescent tints in certain lights. Forewing: the costa, apex and termen bordered with black, this edging narrows from base to the middle of the costa, then broadens greatly at apex, where it occupies the apical fourth of the wing, and is again narrowed below vein 4, whence it is continued as an even band to the tornus; on the disc beyond the apex of the cell the ground colour is sensibly paler, and the dark markings of the cell are faintly visible by transparency from below. Hindwing: the costa very broadly, the termen much more narrowly black; the black bordering on the latter consists of a series of rounded coalescent spots, which on the inner side are margined by faint dark lunules; these are formed not by actual scaling but by the dark markings of the underside which show through more or less clearly.
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The uppersides of its wings are very pale brown in color, somewhat paler in the female, uniform, with the black spots of the underside faintly apparent by transparency. The undersides are white, with round black spots and markings as follows: forewing: a spot at base of wing followed in transverse order by two spots, again two spots, then an irregular row of five spots that crosses near the apex of cell, the lower two coalescent, beyond that another curved row of five spots, two of which are in interspace 3, then a complete curved series of outwardly-pointed and a terminal series of inwardly-pointed similar spots. The spots of the last series cross a well-marked but very slender anteciliary black line, and thus cause the white cilia to the wing to be alternated with black. Hindwing: similarly crossed by five rows, all of which are more or less curved outwards, of black spots, followed by a slender uninterrupted anteciliary black line.
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The Xeelee Sequence (; ) is a series of hard science fiction space opera novels, novellas, and short stories written by British science fiction author Stephen Baxter. The series spans billions of years of fictional history, centering on humanity's future expansion into the universe, its intergalactic war with an enigmatic and supremely powerful Kardashev Type IV alien civilization called the Xeelee, and the Xeelee's own cosmos-spanning war with dark matter entities called Photino Birds. The series features many other species and civilizations that play a prominent role, including the Squeem (a species of group-mind aquatics), the Qax (beings whose biology is based on the complex interactions of convection cells), and the Silver Ghosts (symbiotic organisms encased in reflective shells). Several stories in the Sequence also deal with humans and posthumans living in extreme conditions, such as at the heart of a neutron star (Flux), in a separate universe with considerably stronger gravity (Raft), and within eusocial hive societies (Coalescent).
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The male's upperside is dark brownish black, a broad medial oblique white band across both forewings and hindwings, not extended on the forewing above vein 5, above vein 3 produced shortly outwards and downwards into a hook-like form. Underside: white with the following black markings: On forewing a short, outwardly-pointed, oblique, clavate (club-shaped) streak from base joined below to a semi-circular broad band that reaches the costa; a short, outwardly oblique, upper discal bar, its outer edge generally emarginate; the apex, the termen narrowly, a large irregular sub-quadrate spot touching it in the middle and a very large inwardly oblique irregular spot or mark close to the tornus. On the hindwing: a hook-shaped mark at base sometimes slender; an inwardly oblique short clavate bar from apex, three coalescent spots extended outwards from the dorsum above the tornus formed into a sinuate (sinuous) irregular mark; a spot further outwards in interspace 4; a terminal series of slender lunules and an ancillary fine line. Antennae, head, thorax and abdomen black; beneath: the palpi, thorax and abdomen white. Female.
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Male upperside pale purple to violet with in certain lights a blue suffusion, the markings of the underside apparent through transparency. Forewing: costal margin above vein 12 suffused strongly with blue; discocellulars with a transverse elongate blackish spot; a slender anteciliary black line. Hindwing: immaculate except for an anteciliary black line as on the forewing. Cilia of both forewings and hindwings dull sullied white with a brownish-black band along their bases. Underside: white with the following black markings: Forewing: an anteciliary line continued along the costa but not up to the base; a streak from base passing obliquely to the costa; an obliquely-placed irregular mark across the cell with a spot below it in interspace 1; a curved interrupted band beyond, that consists of a spot in interspace 9 joined to a transverse bar across the discocellulars and detached from it a spot in interspace 2 that coalesces with another in interspace 1; following this are four upper discal spots two and two placed obliquely, the lower two often coalescent, a transverse postdiscal more or less macular curved band, and a subterminal transverse series of six round equal-sized spots.
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Female upperside: dark brown; bases of the wings suffused with bluish scales. Forewing: the transverse discocellular spot as in the 6 but continued posteriorly by a black spot in interspace 2 coalescent with a similar spot in interspace 1 (in some specimens the latter two spots are only seen by transparency from the underside); a medial area beyond apex of cell white, crossed by an upper discal, macular, short black band that extends from vein 3 to vein 6; the ground colour over the rest uniform; on the costal margin there are some pale lines between veins 10, 11 and 12, and on the broad terminal margin of ground colour an obscure transverse macular white line. Hindwing: basal, cellular and discal markings of the underside more or less apparent through transparency; a postdiscal and a subterminal transverse series of white somewhat quadrate spots, the two series converge and meet anteriorly in interspace 6, the outer of the two is margined by the series of black subterminal spots of the underside which show through more or less plainly. Cilia of both forewings and hindwings and tail at apex of vein 2 of the hindwing as in the male.
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Forewing: the markings as on the upperside, but those at apex green and with a few scattered superposed black scales on the upper preapical bar. Hindwing: basal area green, an oval white spot in middle of cell, a transverse white bar in middle of interspace 7, and the precostal area edged with white above; beyond the cell is a highly sinuous, curved, discal, white band, followed by a complete series of longitudinally rectangular, white, terminal spots, the space between the discal band and the white spots green, this colour continued along the veins that separate the spots up to the termen. Antennae, head, thorax and abdomen fuscous, the antennae with pale tips, the thorax with some white hairs; beneath: head, thorax and abdomen whitish. Female differs as follows: Upperside, forewing: the black edging to the discocellulars broader; a curved, postdiscal, irregular, macular, black band, the upper three and lowest spot that compose it large, the spot in inter-space 2 small, sometimes subobsolete, the middle two spots of the band coalescent outwardly with the series of terminal black spots, of which there are six (in the male these vary from 3 to 5).
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