425:, which is the chance of a purine being switched to a pyrimidine, or vice versa. These differences are not captured by maximum parsimony. However, just because some events are more likely than others does not mean that they always happen. We know that throughout evolutionary history there have been times when there was a large gap between what was most likely to happen, and what actually occurred. When this is the case, maximum parsimony may actually be more accurate because it is more willing to make large, unlikely leaps than maximum likelihood is. Maximum likelihood has been shown to be quite reliable in reconstructing character states, but it does not do as good of a job at giving accurate estimations of the stability of proteins. Maximum likelihood always overestimates the stability of proteins, which makes sense since it assumes that the proteins that were made and used were the most stable and optimal. The merits of maximum likelihood have been subject to debate, with some having concluded that maximum likelihood test represents a good medium between accuracy and speed. However, other studies have complained that maximum likelihood takes too much time and computational power to be useful in some scenarios.
3869:, HyPhy, and Mesquite also perform phylogenetic analysis of sequence data, but are designed to be more modular and customizable. HyPhy implements a joint maximum likelihood method of ancestral sequence reconstruction that can be readily adapted to reconstructing a more generalized range of discrete ancestral character states such as geographic locations by specifying a customized model in its batch language. Mesquite provides ancestral state reconstruction methods for both discrete and continuous characters using both maximum parsimony and maximum likelihood methods. It also provides several visualization tools for interpreting the results of ancestral reconstruction. MEGA is a modular system, too, but places greater emphasis on ease-of-use than customization of analyses. As of version 5, MEGA allows the user to reconstruct ancestral states using maximum parsimony, maximum likelihood, and empirical Bayes methods.
2962:. The "genome rearrangement problem", first posed by Watterson and colleagues, asks: given two genomes (permutations) and a set of allowable operations, what is the shortest sequence of operations that will transform one genome into the other? A generalization of this problem applicable to ancestral reconstruction is the "multiple genome rearrangement problem": given a set of genomes and a set of allowable operations, find (i) a binary tree with the given genomes as its leaves, and (ii) an assignment of genomes to the internal nodes of the tree, such that the total number of operations across the whole tree is minimized. This approach is similar to parsimony, except that the tree is inferred along with the ancestral sequences. Unfortunately, even the single genome rearrangement problem is
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never occur; for example, migration between distant locales may never happen directly if air travel between the two places does not exist, so such migrations must pass through intermediate locales first. This means that there could be many parameters in the model which are zero or close to zero. To this end, Lemey and colleagues used a
Bayesian procedure to not only estimate the parameters and ancestral states, but also to select which migration parameters are not zero; their work suggests that this procedure does lead to more efficient use of the data. They also explore the use of prior distributions that incorporate geographical structure or hypotheses about migration dynamics, finding that those they considered had little effect on the findings.
2853:(inferences drawn through comparison of related taxa) are often used to identify biological characteristics that do not evolve independently, which can reveal an underlying dependence. For example, the evolution of the shape of a finch's beak may be associated with its foraging behaviour. However, it is not advisable to search for these associations by the direct comparison of measurements or genetic sequences because these observations are not independent because of their descent from common ancestors. For discrete characters, this problem was first addressed in the framework of maximum parsimony by evaluating whether two characters tended to undergo a change on the same branches of the tree.
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an ancestral state reconstruction for this clade reveals that "hummingbird" is the most parsimonious ancestral state for the lower clade (plants D, E, F), that the ancestral states for the nodes in the top clade (plants A, B, C) are equivocal and that both "hummingbird" or "bee" pollinators are equally plausible for the pollination state at the root of the phylogeny. Supposing we have strong evidence from the fossil record that the root state is "hummingbird". Resolution of the root to "hummingbird" would yield the pattern of ancestral state reconstruction depicted by the symbols at the nodes with the state requiring the fewest changes circled.
847:. It is akin to summing over all combinations of ancestral states at all of the other nodes of the tree (including the root node), other than those for which data is available. Marginal reconstruction is finding the state at the current node that maximizes the likelihood integrating over all other states at all nodes, in proportion to their probability. Second, one may instead attempt to find the joint combination of ancestral character states throughout the tree which jointly maximizes the likelihood of the entire dataset. Thus, this approach is referred to as joint reconstruction. Not surprisingly, joint reconstruction is more
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technique liable to infer that one change occurred on a very short branch rather than multiple changes occurring on a very long branch, for example. In addition, it is possible that some branches of the tree could be experiencing higher selection and change rates than others, perhaps due to changing environmental factors. Some periods of time may represent more rapid evolution than others, when this happens parsimony becomes inaccurate. This shortcoming is addressed by model-based methods (both maximum likelihood and
Bayesian methods) that infer the stochastic process of evolution as it unfolds along each branch of a tree.
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inaccurate. Natural selection and evolution do not work towards a goal, they simply select for or against randomly occurring genetic changes. Parsimony methods impose six general assumptions: that the phylogenetic tree you are using is correct, that you have all of the relevant data, in which no mistakes were made in coding, that all branches of the phylogenetic tree are equally likely to change, that the rate of evolution is slow, and that the chance of losing or gaining a characteristic is the same. In reality, assumptions are often violated, leading to several issues:
410:(ML) methods of ancestral state reconstruction treat the character states at internal nodes of the tree as parameters, and attempt to find the parameter values that maximize the probability of the data (the observed character states) given the hypothesis (a model of evolution and a phylogeny relating the observed sequences or taxa). In other words, this method assumes that the ancestral states are those which are statistically most likely, given the observed phenotypes. Some of the earliest ML approaches to ancestral reconstruction were developed in the context of
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synthetic ancestral sequences obtained by maximum likelihood reconstruction have likewise shown that these ancestors are both functional and immunogenic, lending some credibility to these methods. Furthermore, ancestral reconstruction can potentially be used to infer the genetic sequence of the transmitted HIV variants that have gone on to establish the next infection, with the objective of identifying distinguishing characteristics of these variants (as a non-random selection of the transmitted population of viruses) that may be targeted for vaccine design.
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432:. In the simplest of these, all characters undergo independent state transitions (such as nucleotide substitutions) at a constant rate over time. This basic model is frequently extended to allow different rates on each branch of the tree. In reality, mutation rates may also vary over time (due, for example, to environmental changes); this can be modelled by allowing the rate parameters to evolve along the tree, at the expense of having an increased number of parameters. A model defines transition probabilities from states
274:. Maximum parsimony considers all evolutionary events equally likely; maximum likelihood accounts for the differing likelihood of certain classes of event; and Bayeisan inference relates the conditional probability of an event to the likelihood of the tree, as well as the amount of uncertainty that is associated with that tree. Maximum parsimony and maximum likelihood yield a single most probable outcome, whereas Bayesian inference accounts for uncertainties in the data and yields a sample of possible trees.
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pollination, red representing "hummingbird" pollination, and black representing "wind" pollination, dual coloured branches are equally parsimonious for the two states coloured). Assignment of "hummingbird" as the root state (because of prior knowledge from the fossil record) leads to the pattern of ancestral states represented by symbols at the nodes of the phylogeny, the state requiring the fewest changes to give rise to the pattern observed at the tips is circled at each node.
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their most recent common ancestor is closer to each of the two viruses than they are to each other. Thus, a vaccine designed for a common ancestor could have a better chance of being effective for a larger proportion of circulating strains. Another team took this idea further by developing a center-of-tree reconstruction method to produce a sequence whose total evolutionary distance to contemporary strains is as small as possible. Strictly speaking, this method was not
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2688:, to model the evolution of traits. Stable processes, roughly speaking, behave as Brownian motions that also incorporate discontinuous jumps. This allows to appropriately model scenarios in which short bursts of fast trait evolution are expected. In this setting, maximum likelihood methods are poorly suited due to a rugged likelihood surface and because the likelihood may be made arbitrarily large, so Bayesian methods are more appropriate.
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events happened in the order they did, while recognizing the potential for error and uncertainty. Overall, it is the most accurate method for reconstructing ancestral genetic sequences, as well as protein stability. Unlike the other two methods, Bayesian inference yields a distribution of possible trees, allowing for more accurate and easily interpretable estimates of the variance of possible outcomes.
860:. If the rate of evolution for a specific character accelerates on a branch of the phylogeny, then the amount of evolution that has occurred on that branch will be underestimated for a given length of the branch and assuming a constant rate of evolution for that character. In addition to that, it is difficult to distinguish heterotachy from variation among characters in rates of evolution.
883:. In the context of ancestral reconstruction, the objective is to infer the posterior probabilities of ancestral character states at each internal node of a given tree. Moreover, one can integrate these probabilities over the posterior distributions over the parameters of the evolutionary model and the space of all possible trees. This can be expressed as an application of
3076:. Displayed sequences do not correspond to the original paper, but were derived from the notation in the authors' companion paper as follows: A (63A-65B), B (65C-68D), C (69A-70A), D (70B-70D), E (71A-71B), F (71A-73C), G (74A-74C), H (75A-75C), I (76A-76B), J (76C-77B), K (78A-79D), L (80A-81D). Inversions inferred by the authors are highlighted in blue along branches.
292:", refers to the principle of selecting the simplest of competing hypotheses. In the context of ancestral reconstruction, parsimony endeavours to find the distribution of ancestral states within a given tree which minimizes the total number of character state changes that would be necessary to explain the states observed at the tips of the tree. This method of
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lead to the discoveries of new biochemical functions that have been lost in modern proteins. It also allows insights into the biology and ecology of extinct organisms. Although the majority of ancestral reconstructions have dealt with proteins, it has also been used to test evolutionary mechanisms at the level of bacterial genomes and primate gene sequences.
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missing data includes the states of extinct species, the relative rates of evolutionary changes, knowledge of initial character states, and the accuracy of phylogenetic trees. In all cases where ancestral trait reconstruction is used, findings should be justified with an examination of the biological data that supports model based conclusions. Griffith O.W.
1991:
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fast, and scientifically practical. This concept has been applied to identify co-evolving residues in protein sequences using more advanced methods for the reconstruction of phylogenies and ancestral sequences. For example, ancestral reconstruction has been used to identify co-evolving residues in proteins encoded by RNA virus genomes, particularly in HIV.
1355:. Computationally, the empirical Bayes method is akin to the maximum likelihood reconstruction of ancestral states except that, rather than searching for the ML assignment of states based on their respective probability distributions at each internal node, the probability distributions themselves are reported directly.
2778:". Dietary ancestral state reconstruction using maximum parsimony recover 2 major shifts from an insectivorous state: one to granivory, and one to folivory. Maximum-likelihood ancestral state reconstruction recovers broadly similar results, with one significant difference: the common ancestor of the tree finch (
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444:(in units of evolutionary time). The likelihood of a phylogeny is computed from a nested sum of transition probabilities that corresponds to the hierarchical structure of the proposed tree. At each node, the likelihood of its descendants is summed over all possible ancestral character states at that node:
2442:: in brief, an Ornstein-Uhlenbeck process is a continuous stochastic process that behaves like a Brownian motion, but attracted toward some central value, where the strength of the attraction increases with the distance from that value. This is useful for modelling scenarios where the trait is subject to
330:. In the latter case, it is implied that a character state change has occurred between the ancestor and one of its two immediate descendants. Each such event counts towards the algorithm's cost function, which may be used to discriminate among alternative trees on the basis of maximum parsimony. Next, a
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genomics using ancestral sequence reconstruction. SIMMAP stochastically maps mutations on phylogenies. BayesTraits analyses discrete or continuous characters in a
Bayesian framework to evaluate models of evolution, reconstruct ancestral states, and detect correlated evolution between pairs of traits.
2790:) clades are most likely granivorous rather than insectivorous (as judged by parsimony). In this case, this difference between ancestral states returned by maximum parsimony and maximum likelihood likely occurs as a result of the fact that ML estimates consider branch lengths of the phylogenetic tree.
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is widely used to infer the ecological, phenotypic, or biogeographic traits associated with ancestral nodes in a phylogenetic tree. All methods of ancestral trait reconstructions have pitfalls, as they use mathematical models to predict how traits have changed with large amounts of missing data. This
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Put simply, the empirical Bayes approach calculates the probabilities of various ancestral states for a specific tree and model of evolution. By expressing the reconstruction of ancestral states as a set of probabilities, one can directly quantify the uncertainty for assigning any particular state to
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for ancestral reconstruction require the investigator to assume that the evolutionary model parameters and tree are known without error. When the size or complexity of the data makes this an unrealistic assumption, it may be more prudent to adopt the fully hierarchical
Bayesian approach and infer the
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Parsimony methods implicitly assume that the same amount of evolutionary time has passed along every branch of the tree. Thus, they do not account for variation in branch lengths in the tree, which are often used to quantify the passage of evolutionary or chronological time. This limitation makes the
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For example, consider a phylogeny recovered for a genus of plants containing 6 species A - F, where each plant is pollinated by either a "bee", "hummingbird" or "wind". One obvious question is what the pollinators at deeper nodes were in the phylogeny of this genus of plants. Under maximum parsimony,
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of the entire sample of taxa. In the context of ancestral reconstruction, a phylogeny is often treated as though it were a known quantity (with
Bayesian approaches being an important exception). Because there can be an enormous number of phylogenies that are nearly equally effective at explaining the
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are essentially a variation of ancient ones, access to ancient sequences may identify other variations and organisms which could have arisen from those sequences. In addition to genetic sequences, one might attempt to track the changing of one character trait to another, such as fins turning to legs.
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The development and application of computational algorithms for ancestral reconstruction continues to be an active area of research across disciplines. For example, the reconstruction of sequence insertions and deletions (indels) has lagged behind the more straightforward application of substitution
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of binary character evolution). and BiSSE (Binary State
Speciation and Extinction) models. Lagrange performs analyses on reconstruction of geographic range evolution on phylogenetic trees. Phylomapper is a statistical framework for estimating historical patterns of gene flow and ancestral geographic
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Treating locations as discrete states (countries, cities, etc.) allows for the application of the discrete-state models described above. However, unlike in a model where the state space for the trait is small, there may be many locations, and transitions between certain pairs of states may rarely or
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Ancestral reconstruction is not limited to biological traits. Spatial location is also a trait, and ancestral reconstruction methods can infer the locations of ancestors of the individuals under consideration. Such techniques were used by Lemey and colleagues to geographically trace the ancestors of
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design efforts, as opposed to sequences isolated from patients in the present day. Because HIV is extremely diverse, a vaccine designed to work on one patient's viral population might not work for a different patient, because the evolutionary distance between these two viruses may be large. However,
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reconstruction allows for the recreation of protein and DNA evolution in the laboratory so that it can be studied directly. With respect to proteins, this allows for the investigation of the evolution of present-day molecular structure and function. Additionally, ancestral protein reconstruction can
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ML-based methods of ancestral reconstruction tend to provide greater accuracy than MP methods in the presence of variation in rates of evolution among characters (or across sites in a genome). However, these methods are not yet able to accommodate variation in rates of evolution over time, otherwise
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of the tree is performed, proceeding from the root towards the tips. Character states are then assigned to each descendant based on which character states it shares with its parent. Since the root has no parent node, one may be required to select a character state arbitrarily, specifically when more
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of the genetic composition of a rapidly evolving population, such as RNA viruses or tumour cells, in a relatively short amount of time. At the same time, the massive amount of data and platform-specific sequencing error profiles has created new bioinformatic challenges for processing these data for
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associated with different character states; it may also be straightforwardly extended to a more general multiple-discrete-state model. In its most basic form, this model involves six parameters: two speciation rates (one each for lineages in states 0 and 1); similarly, two extinction rates; and two
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One of the first implementations of a
Bayesian approach to ancestral sequence reconstruction was developed by Yang and colleagues, where the maximum likelihood estimates of the evolutionary model and tree, respectively, were used to define the prior distributions. Thus, their approach is an example
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Rather than compute the overall likelihood for alternative trees, the problem for ancestral reconstruction is to find the combination of character states at each ancestral node with the highest marginal maximum likelihood. Generally speaking, there are two approaches to this problem. First, one can
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from different geographic locations, and observed that one configuration, which they called "standard", was the most common throughout all the studied areas. Remarkably, they also noticed that four different strains could be obtained from the standard sequence by a single inversion, and two others
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Many models have been developed to estimate ancestral states of discrete and continuous characters from extant descendants. Such models assume that the evolution of a trait through time may be modelled as a stochastic process. For discrete-valued traits (such as "pollinator type"), this process is
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Since ML (unlike maximum parsimony) requires the investigator to specify a model of evolution, its accuracy may be affected by the use of a grossly incorrect model (model misspecification). Furthermore, ML can only provide a single reconstruction of character states (what is often referred to as a
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Ancestral reconstruction can be thought of as the direct result of applying a hypothetical model of evolution to a given phylogeny. When the model contains one or more free parameters, the overall objective is to estimate these parameters on the basis of measured characteristics among the observed
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The
Bayesian analysis of genetic sequences may confer greater robustness to model misspecification. MrBayes allows inference of ancestral states at ancestral nodes using the full hierarchical Bayesian approach. The PREQUEL program distributed in the PHAST package performs comparative evolutionary
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reconstruction, as the center-of-tree (COT) sequence does not necessarily represent a sequence that has ever existed in the evolutionary history of the virus. However, Rolland and colleagues did find that, in the case of HIV, the COT virus was functional when synthesized. Similar experiments with
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The reconstruction of ancient proteins and DNA sequences has only recently become a significant scientific endeavour. The developments of extensive genomic sequence databases in conjunction with advances in biotechnology and phylogenetic inference methods have made ancestral reconstruction cheap,
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identified this problem for continuous character evolution and proposed a solution similar to ancestral reconstruction, in which the phylogenetic structure of the data was accommodated statistically by directing the analysis through computation of "independent contrasts" between nodes of the tree
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In the case where the trait instead takes non-discrete values, one must instead turn to a model where the trait evolves as some continuous process. Inference of ancestral states by maximum likelihood (or by
Bayesian methods) would proceed as above, but with the likelihoods of transitions in state
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states; when it reaches a given state, it starts an exponential "clock" for each of the other states that it can step to. It then "races" the clocks against each other, and it takes a step towards the state whose clock is the first to ring. In such a model, the parameters are the transition rates
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Ancestral reconstruction can be informed by the observed states in historical samples of known age, such as fossils or archival specimens. Since the accuracy of ancestral reconstruction generally decays with increasing time, the use of such specimens provides data that are closer to the ancestors
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Bayesian inference is the method that many have argued is the most accurate. In general, Bayesian statistical methods allow investigators to combine pre-existing information with new hypothesis. In the case of evolution, it combines the likelihood of the data observed with the likelihood that the
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Phylogeny of a hypothetical genus of plants with pollination states of either "bees", "hummingbirds" or "wind" denoted by pictures at the tips. Pollination state nodes in the phylogenetic tree inferred under maximum parsimony are coloured on the branches leading into them (yellow represents "bee"
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has taken and when evolutionary events occurred. No matter how well the model approximates the actual evolutionary history, however, one's ability to accurately reconstruct an ancestor deteriorates with increasing evolutionary time between that ancestor and its observed descendants. Additionally,
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of continuous character evolution, which accommodates rare changes of large magnitude. Under a stable model, ancestral mammals retained a low body mass through early diversification, with large increases in body mass coincident with the origin of several Orders of large body massed species (e.g.
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When considering a single character state, parsimony will automatically assume that two organisms that share that characteristic will be more closely related than those who do not. For example, just because dogs and apes have fur does not mean that they are more closely related than apes are to
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analysis (DIVA; parsimony), and dispersal-extinction-cladogenesis (DEC; maximum-likelihood). Results indicated that both parsimony methods performed poorly, which was likely due to the fact that parsimony methods do not consider branch lengths. Both maximum-likelihood methods performed better;
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Finally, there are several web-server based applications that allow investigators to use maximum likelihood methods for ancestral reconstruction of different character types without having to install any software. For example, Ancestors is web-server for ancestral genome reconstruction by the
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between species. ANGES compares extant related genomes through ancestral reconstruction of genetic markers. BADGER uses a
Bayesian approach to examining the history of gene rearrangement. Count reconstructs the evolution of the size of gene families. EREM analyses the gain and loss of genetic
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at different locations of a protein may evolve non-independently because they have a direct physicochemical interaction, or indirectly by their interactions with a common substrate or through long-range interactions in the protein structure. Conversely, the folded structure of a protein could
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from the posterior likelihood, and prior terms of the formula. Moreover, Yang and colleagues used the empirical distribution of site patterns (i.e., assignments of nucleotides to tips of the tree) in their alignment of observed nucleotide sequences in the denominator in place of exhaustively
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Thus, ancestral reconstruction has its roots in several disciplines. Today, computational methods for ancestral reconstruction continue to be extended and applied in a diversity of settings, so that ancestral states are being inferred not only for biological characteristics and the molecular
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Another maximum likelihood method recovers the phylogeographic history of a gene by reconstructing the ancestral locations of the sampled taxa. This method assumes a spatially explicit random walk model of migration to reconstruct ancestral locations given the geographic coordinates of the
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Parsimony methods are intuitively appealing and highly efficient, such that they are still used in some cases to seed maximum likelihood optimization algorithms with an initial phylogeny. However, the underlying assumption that evolution attained a certain end result as fast as possible is
175:, one of the precursors of modern phylogenetics. Cladistic methods, which appeared as early as 1901, infer the evolutionary relationships of species on the basis of the distribution of shared characteristics, of which some are inferred to be descended from common ancestors. Furthermore,
3897:' function, including maximum likelihood. Phyrex implements a maximum parsimony-based algorithm to reconstruct ancestral gene expression profiles, in addition to a maximum likelihood method for reconstructing ancestral genetic sequences (by wrapping around the baseml function in PAML).
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is an important exception to this paradigm: though it has been shown that there are circumstances under which it is the maximum likelihood estimator, at its core, it is simply based on the heuristic that changes in character state are rare, without attempting to quantify that rarity.
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models. Bouchard-Cรดtรฉ and Jordan recently described a new model (the Poisson Indel Process) which represents an important advance on the archetypal Thorne-Kishino-Felsenstein model of indel evolution. In addition, the field is being driven forward by rapid advances in the area of
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The majority of these software packages are designed for analyzing genetic sequence data. For example, PAML is a collection of programs for the phylogenetic analysis of DNA and protein sequence alignments by maximum likelihood. Ancestral reconstruction can be performed using the
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Griffith OW, Blackburn DG, Brandley MC, Van Dyke JU, Whittington CM, Thompson MB (September 2015). "Ancestral state reconstructions require biological evidence to test evolutionary hypotheses: A case study examining the evolution of reproductive mode in squamate reptiles".
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1408:); these results were verified by computer simulation. This failure of ancestral reconstruction was attributed to a directional bias in the evolution of plaque size (from large to small plaque diameters) that required the inclusion of "fossilized" samples to address.
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ungulates). By contrast, simulation under a Brownian motion model recovered a less realistic, order of magnitude larger body mass among ancestral mammals, requiring significant reductions in body size prior to the evolution of Orders exhibiting small body size (e.g.
1509:. The typical means of modelling evolution of this trait is via a continuous-time Markov chain, which may be briefly described as follows. Each state has associated to it rates of transition to all of the other states. The trait is modelled as stepping between the
3132:. The following table is not meant to be a comprehensive itemization of all available packages, but provides a representative sample of the extensive variety of packages that implement methods of ancestral reconstruction with different strengths and features.
2911:(HIV) evolve at an extremely rapid rate, orders of magnitude faster than mammals or birds. For these organisms, ancestral reconstruction can be applied on a much shorter time scale; for example, in order to reconstruct the global or regional progenitor of an
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relating the observed protein sequences, but also the ancestral protein sequence at the earliest point (root) of this tree. However, the idea of reconstructing ancestors from measurable biological characteristics had already been developing in the field of
1753:; finally, choose the ancestral state which maximizes this. One may also use this substitution model as the basis for a Bayesian inference procedure, which would consider the posterior belief in the state of an ancestral node given some user-chosen prior.
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that has already been inferred from the same data. While convenient, this approach has the disadvantage that its results are contingent on the accuracy of a single phylogenetic tree. In contrast, some researchers advocate a more computationally intensive
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Pupko T, Pe'er I, Hasegawa M, Graur D, Friedman N (August 2002). "A branch-and-bound algorithm for the inference of ancestral amino-acid sequences when the replacement rate varies among sites: Application to the evolution of five gene families".
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Whether the hierarchical Bayes method confers a substantial advantage in practice remains controversial, however. Moreover, this fully Bayesian approach is limited to analyzing relatively small numbers of sequences or taxa because the space of
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Fitch's method assumes that changes between all character states are equally likely to occur; thus, any change incurs the same cost for a given tree. This assumption is often unrealistic and can limit the accuracy of such methods. For example,
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were propagated to generate an artificial phylogeny. In revisiting these experimental data, Oakley and Cunningham found that maximum parsimony methods were unable to accurately reconstruct the known ancestral state of a continuous character
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Studies of both mammalian carnivores and fishes have demonstrated that without incorporating fossil data, the reconstructed estimates of ancestral body sizes are unrealistically large. Moreover, Graham Slater and colleagues showed using
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an ancestor. On the other hand, the hierarchical Bayes approach averages these probabilities over all possible trees and models of evolution, in proportion to how likely these trees and models are, given the data that has been observed.
892:
450:
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though Brownian motion is appealing and tractable as a model of continuous evolution, it does not permit non-neutrality in its basic form, nor does it provide for any variation in the rate of evolution over time. Instead, one may use a
1862:, regardless of their start and end states. Some transitions may be disallowed by declaring that their rates are simply 0; this may be the case, for example, if certain states cannot be reached from other states in a single transition.
864:"point estimate") — when the likelihood surface is highly non-convex, comprising multiple peaks (local optima), then a single point estimate cannot provide an adequate representation, and a Bayesian approach may be more suitable.
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Rather than inferring the ancestral DNA sequence, one may be interested in the larger-scale molecular structure and content of an ancestral genome. This problem is often approached in a combinatorial framework, by modelling genomes as
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There are many software packages available which can perform ancestral state reconstruction. Generally, these software packages have been developed and maintained through the efforts of scientists in related fields and released under
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being reconstructed and will most likely improve the analysis, especially when rates of character change vary through time. This concept has been validated by an experimental evolutionary study in which replicate populations of
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The binary state speciation and extinction model (BiSSE) is a discrete-space model that does not directly follow the framework of those mentioned above. It allows estimation of ancestral binary character states jointly with
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locations. RASP infers ancestral states using statistical dispersal-vicariance analysis, Lagrange, Bayes-Lagrange, BayArea and BBM methods. VIP infers historical biogeography by examining disjunct geographic distributions.
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have been performed based on the observed analogues in present-day languages. Typically, these analyses are carried out manually using the "comparative method". First, words from different languages with a common etymology
1897:: in this model, the state space is ordered (so that, for example, state 1 is smaller than state 2, which is smaller than state 3), and transitions may only occur between adjacent states. This model contains two parameters
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The first consideration of the multiple genome rearrangement problem, long before its formalization in terms of permutations, was presented by Sturtevant and Dobzhansky in 1936. They examined genomes of several strains of
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Example of a four-state 1-parameter Markov chain model. Note that in this diagram, transitions between states A and D have been disallowed; it is conventional to not draw the arrow rather than to draw it with a rate of
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was used together with information of their geographic ranges to compare four methods of ancestral range reconstruction. The team compared Fitch parsimony, (FP; parsimony) stochastic mapping (SM; maximum likelihood),
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to compute the posterior probabilities of ancestral character states; this method was first implemented in the software package PAML. In terms of the above Bayesian rule formulation, the empirical Bayes method fixes
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technology, where sequences are generated from millions of nucleic acid templates by extensive parallelization of sequencing reactions in a custom apparatus. These advances have made it possible to generate a
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Cooper, N., G. H. Thomas, C. Venditti, A. Meade, and R. P. Freckleton. 2015. A cautionary note on the use of Ornstein Uhlenbeck models in macroevolutionary studies. Biological Journal of the Linnean Society.
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2762:. These data allow testing of hypotheses concerning the timing and ordering of character state changes through time via ancestral state reconstruction. During the dry season, the diets of the 13 species of
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than marginal reconstruction. Nevertheless, efficient algorithms for joint reconstruction have been developed with a time complexity that is generally linear with the number of observed taxa or sequences.
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reconstruction. Chromosome painting is currently the main experimental technique. Recently, researchers have developed computational methods to reconstruct the ancestral karyotype by taking advantage of
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that incorporating fossil data into prior distributions improved both the Bayesian inference of ancestral states and evolutionary model selection, relative to analyses using only contemporaneous data.
7604:"Human immunodeficiency virus type 1 subtype B ancestral envelope protein is functional and elicits neutralizing antibodies in rabbits similar to those elicited by a circulating subtype B envelope"
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These approaches employ the same probabilistic framework as used to infer the phylogenetic tree. In brief, the evolution of a genetic sequence is modelled by a time-reversible continuous time
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Murphy WJ, Larkin DM, Everts-van der Wind A, Bourque G, Tesler G, Auvil L, et al. (July 2005). "Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps".
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Erkenbrack EM, Ako-Asare K, Miller E, Tekelenburg S, Thompson JR, Romano L (January 2016). "Ancestral state reconstruction by comparative analysis of a GRN kernel operating in echinoderms".
1366:(MCMC) methods to sample ancestral sequences from this joint posterior distribution. A similar approach was also used to reconstruct the evolution of symbiosis with algae in fungal species (
3061:, this method recovered recent northward expansion, higher per-generation dispersal distance in the recently colonized region, a non-central ancestral location, and directional migration.
2978:. Furthermore, comparative genomics and ancestral genome reconstruction has been applied to identify ancient horizontal gene transfer events at the last common ancestor of a lineage (e.g.
2436:), and the model assumes that the trait evolves freely without a bias toward increase or decrease, and that the rate of change is constant throughout the branches of the phylogenetic tree.
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joint posterior distribution over the ancestral character states, model, and tree. Huelsenbeck and Bollback first proposed a hierarchical Bayes method to ancestral reconstruction by using
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and the process becomes a Brownian motion. Because of this, the models may be nested, and log-likelihood ratio tests discerning which of the two models is appropriate may be carried out.
9629:
6245:
Finarelli JA, Flynn JJ (April 2006). "Ancestral state reconstruction of body size in the Caniformia (Carnivora, Mammalia): the effects of incorporating data from the fossil record".
9624:
3086:
could be related by a second inversion. This allowed them to hypothesize a phylogeny for the sequences, and to infer that the standard sequence was probably also the ancestral one.
2817:, one of the three main subclades of the lineage, have undergone a major evolutionary increase in the proportion of fast-oxidative glycolytic fibers in their iliofibularis muscles.
1670:
311:
that proceeds from the tips toward the root of a tree by visiting descendant (child) nodes before their parents. Initially, we are determining the set of possible character states
2716:, developmental gene expression, and functional divergence of the evolutionary past. For a review of biological and computational techniques of ancestral reconstruction see Chang
368:
in the evolution of nucleic acids. This assumption can be relaxed by assigning differential costs to specific character state changes, resulting in a weighted parsimony algorithm.
250:
data, reducing the subset of phylogenies supported by the data to a single representative, or point estimate, can be a convenient and sometimes necessary simplifying assumption.
237:
of the tree that are progressively connected by branches to their common ancestors, which are represented by the branching points of the tree that are usually referred to as the
6933:
Maddison WP (May 1990). "A Method for Testing the Correlated Evolution of Two Binary Characters: Are Gains or Losses Concentrated on Certain Branches of a Phylogenetic Tree?".
1978:
rates of character change. This model allows for hypothesis testing on the rates of speciation/extinction/character change, at the cost of increasing the number of parameters.
2875:
through residue contacts, was published by Shindyalov and colleagues. Phylogenies relating 67 different protein families were generated by a distance-based clustering method (
3115:, although performed manually. Finally, likely ancestral sounds are hypothesised by manual inspection and various heuristics (such as the fact that most languages have both
1953:
1924:
1160:
2140:
2078:
2045:
2407:
1692:
1610:, which can be estimated using, for example, maximum likelihood methods, where one maximizes over the set of all possible configurations of states of the ancestral nodes.
1238:
1201:
2571:
2434:
2169:
1507:
2107:
6883:
Bonine KE, Gleeson TT, Garland T (December 2005). "Muscle fiber-type variation in lizards (Squamata) and phylogenetic reconstruction of hypothesized ancestral states".
803:
is the set of all possible character states (for example, the nucleotides A, C, G, and T). Thus, the objective of ancestral reconstruction is to find the assignment to
54:, ancestral reconstruction can be used to recover different kinds of ancestral character states of organisms that lived millions of years ago. These states include the
1082:{\displaystyle {\begin{aligned}P(S|D,\theta )&={\frac {P(D|S,\theta )P(S|\theta )}{P(D|\theta )}}\\&\propto P(D|S,\theta )P(S|\theta )P(\theta )\end{aligned}}}
688:{\displaystyle L_{x}=\sum _{S_{x}\in \Omega }P(S_{x})\left(\sum _{S_{y}\in \Omega }P(S_{y}|S_{x},t_{xy})L_{y}\sum _{S_{z}\in \Omega }P(S_{z}|S_{x},t_{xz})L_{z}\right)}
117:
more realistic models of evolution are inevitably more complex and difficult to calculate. Progress in the field of ancestral reconstruction has relied heavily on the
2631:
2591:
1712:
1639:
1353:
1299:
1279:
1117:
801:
1789:
773:
2842:). Thus stable models recover a more realistic picture of mammalian body mass evolution by permitting large transformations to occur on a small subset of branches.
828:
739:
8943:
Arias JS, Szumik CA, Goloboff PA (December 2011). "Spatial analysis of vicariance: a method for using direct geographical information in historical biogeography".
1329:
3942:
regions. FastML is a web-server for probabilistic reconstruction of ancestral sequences by maximum likelihood that uses a gap character model for reconstructing
9123:"EREM: Parameter Estimation and Ancestral Reconstruction by Expectation-Maximization Algorithm for a Probabilistic Model of Genomic Binary Characters Evolution"
3035:
patterns often requires reconstructing ancestral ranges of species on phylogenetic trees. For instance, a well-resolved phylogeny of plant species in the genus
2671:
2651:
2611:
2544:
2524:
2504:
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2217:
2197:
2012:
1893:
1860:
1836:
1814:
1527:
1475:
7019:
Shindyalov IN, Kolchanov NA, Sander C (March 1994). "Can three-dimensional contacts in protein structures be predicted by analysis of correlated mutations?".
3929:
features encoded by binary characters. PARANA performs parsimony based inference of ancestral biological networks that represent gene loss and duplication.
1617:
A general two-state Markov chain representing the rate of jumps from allele a to allele A. The different types of jumps are allowed to have different rates.
843:
assign the most likely character state to each ancestor independently of the reconstruction of all other ancestral states. This approach is referred to as
1374:
for MCMC explores the joint posterior distribution by accepting or rejecting parameter assignments on the basis of the ratio of posterior probabilities.
4365:
Brooks DR (1999). "Phylogenies and the Comparative Method in Animal Behavior, Edited by Emฤฑฬia P. Martins, Oxford University Press, 1996. X+415 pp".
2915:
that has spanned decades rather than millions of years. A team around Brian Gaschen proposed that such reconstructed strains be used as targets for
2871:
potentially be inferred from the distribution of residue interactions. One of the earliest applications of ancestral reconstruction, to predict the
7216:
Jermann TM, Opitz JG, Stackhouse J, Benner SA (March 1995). "Reconstructing the evolutionary history of the artiodactyl ribonuclease superfamily".
3377:
1839:
7369:"Genome diversification in phylogenetic lineages I and II of Listeria monocytogenes: identification of segments unique to lineage II populations"
1955:: one for the rate of increase of state (e.g. 0 to 1, 1 to 2, etc.), and one for the rate of decrease in state (e.g. from 2 to 1, 1 to 0, etc.).
429:
6202:
Oakley TH, Cunningham CW (April 2000). "Independent contrasts succeed where ancestor reconstruction fails in a known bacteriophage phylogeny".
3866:
1247:
We have given two formulations above to emphasize the two different applications of Bayes' theorem, which we discuss in the following section.
6772:
Chang BS, Ugalde JA, Matz MV (2005). "Applications of ancestral protein reconstruction in understanding protein function: GFP-like proteins".
5880:"Difficulties in testing for covarion-like properties of sequences under the confounding influence of changing proportions of variable sites"
6856:
Maddison WP (1991). "Squared-change parsimony reconstructions of ancestral states for continuous-valued characters on a phylogenetic tree".
8892:
Yu Y, Harris AJ, He X (August 2010). "S-DIVA (Statistical Dispersal-Vicariance Analysis): A tool for inferring biogeographic histories".
5243:
Felsenstein J (1973). "Maximum Likelihood and Minimum-Steps Methods for Estimating Evolutionary Trees from Data on Discrete Characters".
3865:
scripts that wrap the ancestral reconstruction functions of PAML for batch processing and greater ease-of-use. Software packages such as
3047:
however, DEC analyses that additionally allow incorporation of geological priors gave more realistic inferences about range evolution in
8277:"Inversions in the Third Chromosome of Wild Races of Drosophila Pseudoobscura, and Their Use in the Study of the History of the Species"
9634:
8841:
Pagel M (1994). "Detecting Correlated Evolution on Phylogenies: A General Method for the Comparative Analysis of Discrete Characters".
421:, which is a type of point mutation from one purine to another, or from one pyrimidine to another is much more likely to happen than a
7457:
Gaschen B, Taylor J, Yusim K, Foley B, Gao F, Lang D, et al. (June 2002). "Diversity considerations in HIV-1 vaccine selection".
1533:
6159:
Hillis DM, Bull JJ, White ME, Badgett MR, Molineux IJ (January 1992). "Experimental phylogenetics: generation of a known phylogeny".
3912:
provides tools for reconstructing ancestral geographic locations from observed sequences annotated with location data using Bayesian
3111:
biological sequences. Second, correspondences between individual sounds in the cognates are identified, a step similar to biological
183:
articulated the principles of ancestral reconstruction in a phylogenetic context in 1938, when inferring the evolutionary history of
7056:"Covariation of mutations in the V3 loop of human immunodeficiency virus type 1 envelope protein: an information theoretic analysis"
5387:
Li G, Steel M, Zhang L (August 2008). "More taxa are not necessarily better for the reconstruction of ancestral character states".
4968:
Tuffley C, Steel M (May 1997). "Links between maximum likelihood and maximum parsimony under a simple model of site substitution".
2833:
models, Elliot and Mooers showed that the evolutionary process describing mammalian body mass evolution is best characterized by a
82:
of an ancestral population or species (ancestral range reconstruction). This is desirable because it allows us to examine parts of
6280:
Albert JS, Johnson DM, Knouft JH (2009). "Fossils provide better estimates of ancestral body size than do extant taxa in fishes".
5699:
4029:
1163:
7997:"Ancestral genome reconstruction identifies the evolutionary basis for trait acquisition in polyphosphate accumulating bacteria"
4421:
Pupko T, Pe'er I, Shamir R, Graur D (June 2000). "A fast algorithm for joint reconstruction of ancestral amino acid sequences".
7653:"An evaluation of phylogenetic methods for reconstructing transmitted HIV variants using longitudinal clonal HIV sequence data"
3019:
also receiving posterior support. Further, their results support the hypothesis of long-standing presence of African rabies in
9433:
Thorne JL, Kishino H, Felsenstein J (August 1991). "An evolutionary model for maximum likelihood alignment of DNA sequences".
5342:
Mooers Aร, Schluter D (1999). "Reconstructing Ancestor States with Maximum Likelihood: Support for One- and Two-Rate Models".
6574:"Inferring ancestral states without assuming neutrality or gradualism using a stable model of continuous character evolution"
3612:
2879:, UPGMA), and ancestral sequences were reconstructed by parsimony. The authors reported a weak but significant tendency for
5291:
Cunningham CW, Omland KE, Oakley TH (September 1998). "Reconstructing ancestral character states: a critical reappraisal".
3430:
6813:
Hodges WL (November 2004). "Evolution of viviparity in horned lizards (Phrynosoma): testing the cold-climate hypothesis".
2950:(a segment is removed from one part of the permutation and spliced in somewhere else), or gain of genetic content through
108:
to accurately recover ancestral states. These models use the genetic information already obtained through methods such as
8397:
2966:, although it has received much attention in mathematics and computer science (for a review, see Fertin and colleagues).
262:
There are three different classes of method for ancestral reconstruction. In chronological order of discovery, these are
5700:"Computational aspects of maximum likelihood estimation of autoregressive fractionally integrated moving average models"
1717:
9037:
Larget B, Kadane JB, Simon DL (August 2005). "A Bayesian approach to the estimation of ancestral genome arrangements".
7418:"Ancestral sequence reconstruction in primate mitochondrial DNA: compositional bias and effect on functional inference"
3491:
417:
The use of a model of evolution accounts for the fact that not all events are equally likely to happen. For example, a
142:
approach that accounts for uncertainty in tree reconstruction by evaluating ancestral reconstructions over many trees.
8059:"A comparative study in ancestral range reconstruction methods: retracing the uncertain histories of insular lineages"
3818:
7795:
7115:"A phylogenetic method for detecting positive epistasis in gene sequences and its application to RNA virus evolution"
6789:
6529:
Garland Jr T, Dickerman AW, Janis CM, Jones JA (1993). "Phylogenetic analysis of covariance by computer simulation".
4005:
3211:
374:
The upshot of the "minimum evolution" heuristic underlying such methods is that such methods assume that changes are
59:
5608:"The Maximum Likelihood Approach to Reconstructing Ancestral Character States of Discrete Characters on Phylogenies"
2850:
34:) is the extrapolation back in time from measured characteristics of individuals, populations, or species to their
6976:
Gรถbel U, Sander C, Schneider R, Valencia A (April 1994). "Correlated mutations and residue contacts in proteins".
3893:
also provides methods for ancestral state reconstruction for both discrete and continuous characters through the '
3055:
individuals represented by the tips of the phylogenetic tree. When applied to a phylogenetic tree of chorus frogs
296:
is one of the earliest formalized algorithms for reconstructing ancestral states, as well as one of the simplest.
5200:
Schluter D, Price T, Mooers Aร, Ludwig D (December 1997). "Likelihood of Ancestor States in Adaptive Radiation".
848:
6215:
3916:
sampling methods. Diversitree is an R package providing methods for ancestral state reconstruction under Mk2 (a
2546:
would have a likelihood defined by the transition density of an Ornstein-Uhlenbeck process with two parameters:
86:
corresponding to the distant past, clarifying the evolutionary history of the species in the tree. Since modern
6014:
Huelsenbeck JP, Bollback JP (June 2001). "Empirical and hierarchical Bayesian estimation of ancestral states".
3317:
2997:
3064:
9644:
6059:
Lutzoni F, Pagel M, Reeb V (June 2001). "Major fungal lineages are derived from lichen symbiotic ancestors".
4811:"Maximum likelihood inference of geographic range evolution by dispersal, local extinction, and cladogenesis"
3862:
2766:
may be assorted into three broad diet categories, first those that consume grain-like foods are considered "
326:
of the character states of the ancestor's descendants; if the intersection is the empty set, then it is the
7848:"Are molecular cytogenetics and bioinformatics suggesting diverging models of ancestral mammalian genomes?"
3917:
3099:
1644:
1240:
is the probability of the data for a given model and tree, integrated over all possible ancestral states.
6720:"Cell type phylogenetics informs the evolutionary origin of echinoderm larval skeletogenic cell identity"
5059:
Fitch WM (1971). "Toward Defining the Course of Evolution: Minimum Change for a Specific Tree Topology".
3982:
699:
246:
133:
reconstruction of ancestral sequences). Methods of ancestral reconstruction are often applied to a given
391:
Without a statistical model underlying the method, its estimates do not have well-defined uncertainties.
5542:
Koshi JM, Goldstein RA (February 1996). "Probabilistic reconstruction of ancestral protein sequences".
4204:
Platnick NI, Cameron HD (1977). "Cladistic Methods in Textual, Linguistic, and Phylogenetic Analysis".
4044:
3956:
3881:
Other software packages are more oriented towards the analysis of qualitative and quantitative traits (
3265:
3238:
3183:
2872:
1438:
1383:
8692:"Phylogenetic reconstruction of ancestral character states for gene expression and mRNA splicing data"
7510:"Reconstruction and function of ancestral center-of-tree human immunodeficiency virus type 1 proteins"
5104:"RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models"
5564:
5021:
Swofford DL, Maddison WP (1987). "Reconstructing ancestral character states under Wagner parsimony".
323:
8366:
8239:
8116:
7159:"An evolutionary-network model reveals stratified interactions in the V3 loop of the HIV-1 envelope"
6431:
6028:
5665:
5160:
4827:
4479:
3480:
3011:
Using this analysis, the team around Lemey found that the most likely hub of diffusion of A-H5N1 is
2809:. Ancestor reconstruction based on squared-change parsimony (equivalent to maximum likelihood under
1929:
1900:
1122:
166:
in 1955, Zuckerkandl and Pauling postulated that such sequences could be used to infer not only the
7846:
Froenicke L, Caldรฉs MG, Graphodatsky A, Mรผller S, Lyons LA, Robinson TJ, et al. (March 2006).
5356:
4982:
3913:
3890:
3345:
3082:
2959:
2951:
2112:
2050:
2017:
1387:
1363:
299:
Maximum parsimony can be implemented by one of several algorithms. One of the earliest examples is
189:
98:, and cultural characteristics of ancient societies such as oral traditions or marriage practices.
7557:
Kothe DL, Li Y, Decker JM, Bibollet-Ruche F, Zammit KP, Salazar MG, et al. (September 2006).
7114:
5791:
Eyre-Walker A (December 1998). "Problems with parsimony in sequences of biased base composition".
3673:
3392:
2382:
1791:
parameters, overfitting may be an issue. Some common choices that reduce the parameter space are:
1675:
1206:
1169:
3108:
2938:
of genes or homologous regions. Various operations are allowed on these permutations, such as an
2549:
2412:
2145:
1480:
2083:
8361:
8234:
8111:
6426:
6023:
5660:
5559:
5351:
5155:
4977:
4822:
4474:
4033:
3107:) are identified in the contemporary languages under study, analogous to the identification of
1358:
1257:
322:-th ancestor based on the observed character states of its descendants. Each assignment is the
9264:
Ashkenazy H, Penn O, Doron-Faigenboim A, Cohen O, Cannarozzi G, Zomer O, Pupko T (July 2012).
8790:
FitzJohn RG (2012). "Diversitree: comparative phylogenetic analyses of diversification in R".
8169:"A likelihood framework for inferring the evolution of geographic range on phylogenetic trees"
7787:
6366:"Testing the accuracy of methods for reconstructing ancestral states of continuous characters"
5740:
Felsenstein J (1981). "Evolutionary trees from DNA sequences: a maximum likelihood approach".
3716:
1281:
to the empirical estimates of the model and tree obtained from the data, effectively dropping
7995:
Oyserman BO, Moya F, Lawson CE, Garcia AL, Vogt M, Heffernen M, et al. (December 2016).
3129:
3073:
2939:
2883:
pairs of residues to be co-located in the known three-dimensional structure of the proteins.
2616:
2576:
1974:
1697:
1624:
1338:
1284:
1264:
1102:
880:
786:
418:
414:; similar models were also developed for the analogous case of discrete character evolution.
361:
184:
176:
55:
5649:"A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood"
1759:
748:
308:
9573:
9501:
9485:
9442:
9387:
9046:
8901:
8850:
8799:
8288:
8008:
7904:
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7225:
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6641:
6585:
6168:
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4934:
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4723:
4319:
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3990:
3925:
3829:
2975:
2947:
806:
717:
331:
79:
51:
9490:"Reconstructing the dynamics of HIV evolution within hosts from serial deep sequence data"
7344:
7327:
4434:
1305:
8:
8223:"A likelihood framework for estimating phylogeographic history on a continuous landscape"
6467:
Martins EP (1994). "'Estimating the rate of phenotypic evolution from comparative data".
4038:
Jeffrey B Joy; Richard H Liang; Rosemary M McCloskey; T Nguyen; Art Poon (12 July 2016).
3245:
2943:
2834:
2763:
2713:
2685:
1621:
In order to recover the state of a given ancestral node in the phylogeny (call this node
1371:
411:
378:, and thus are inappropriate in cases where change is the norm rather than the exception.
139:
126:
9577:
9505:
9446:
9391:
9050:
8905:
8854:
8803:
8292:
8012:
7908:
7741:
Even S, Goldreich O (1981). "The minimum-length generator sequence problem is NP-hard".
7470:
7284:
7229:
7174:
7071:
6645:
6589:
6172:
6072:
5804:
5753:
5555:
5304:
4938:
4880:
4727:
4323:
4264:
94:
Non-biological applications include the reconstruction of the vocabulary or phonemes of
9596:
9563:
9551:
9524:
9489:
9466:
9410:
9377:
9365:
9341:
9314:
9290:
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9200:
9173:
9149:
9122:
8978:
8925:
8874:
8823:
8767:
8742:
8718:
8691:
8652:
8625:
8601:
8576:
8511:
8486:
8311:
8276:
8198:
8185:
8168:
8029:
7996:
7972:
7947:
7928:
7872:
7847:
7677:
7652:
7628:
7619:
7603:
7534:
7509:
7490:
7303:
7268:
7249:
7193:
7158:
7001:
6950:
6920:
The explanation of organic diversity: the comparative method and adaptations for mating
6838:
6746:
6719:
6700:
6608:
6573:
6484:
6390:
6365:
6346:
6227:
6136:
6111:
6092:
5856:
5824:
5773:
5585:
5519:
5494:
5468:
5422:
5396:
5324:
5268:
5217:
5084:
5003:
4899:
4864:
4746:
4711:
4680:
4655:
4631:
4606:
4538:
4513:
4398:
4342:
4307:
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4229:
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3112:
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1997:
1878:
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1821:
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1512:
1460:
1446:
1442:
872:
407:
327:
303:, which assigns ancestral character states by parsimony via two traversals of a rooted
271:
267:
130:
105:
7718:
7701:
7508:
Rolland M, Jensen MA, Nickle DC, Yan J, Learn GH, Heath L, et al. (August 2007).
7393:
7368:
6781:
6317:"Integrating fossils with molecular phylogenies improves inference of trait evolution"
5988:
5971:
5947:
5930:
5715:
5312:
4925:
Watterson GA, Ewens WJ, Hall TE, Morgan A (1982). "The chromosome inversion problem".
4378:
4181:
4154:
3777:
3766:
1961:
Graphical representation of an asymmetrical five-state 2-parameter Markov chain model.
1203:
is the prior probability of the ancestral states for a given model and tree. Finally,
9601:
9547:
9529:
9458:
9415:
9346:
9295:
9246:
9205:
9154:
9103:
9082:"Count: evolutionary analysis of phylogenetic profiles with parsimony and likelihood"
9062:
9019:
8970:
8956:
8917:
8866:
8815:
8811:
8772:
8723:
8657:
8606:
8557:
8516:
8449:
8379:
8316:
8254:
8190:
8131:
8080:
8034:
7977:
7920:
7877:
7828:
7791:
7777:
7758:
7754:
7723:
7682:
7633:
7580:
7539:
7482:
7439:
7398:
7384:
7367:
Zhang C, Zhang M, Ju J, Nietfeldt J, Wise J, Terry PM, et al. (September 2003).
7349:
7308:
7241:
7198:
7139:
7095:
7090:
7055:
7036:
6993:
6958:
6900:
6830:
6826:
6795:
6785:
6751:
6692:
6657:
6613:
6515:
6446:
6395:
6338:
6333:
6316:
6297:
6293:
6262:
6231:
6219:
6184:
6141:
6084:
6041:
5993:
5952:
5911:
5860:
5816:
5765:
5719:
5680:
5629:
5577:
5524:
5460:
5414:
5369:
5316:
5260:
5225:
5173:
5128:
5076:
5038:
5034:
5007:
4995:
4950:
4946:
4904:
4842:
4786:
4751:
4685:
4636:
4584:
4579:
4562:
4543:
4494:
4438:
4390:
4382:
4347:
4288:
4221:
4186:
4135:
4081:
4063:
3069:
3037:
2982:
Accumulibacter phosphatis) to identify the evolutionary basis for trait acquisition.
2759:
884:
876:
293:
283:
263:
229:) are related by descent from common ancestors. Observed taxa are represented by the
180:
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102:
83:
9470:
9241:
9224:
9098:
9081:
9014:
8997:
8982:
8929:
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8827:
8552:
8535:
8444:
8427:
8202:
7932:
7494:
7005:
6842:
6488:
6350:
5828:
5589:
5123:
5103:
4017:
3352:
2746:(live birth) has evolved multiple times, based on ancestral reconstruction methods.
834:
internal nodes that maximizes the likelihood of the observed data for a given tree.
9591:
9581:
9519:
9509:
9450:
9405:
9395:
9336:
9326:
9285:
9277:
9236:
9195:
9185:
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9134:
9093:
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8952:
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8713:
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8371:
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8121:
8070:
8024:
8016:
7967:
7959:
7946:
Ma J, Zhang L, Suh BB, Raney BJ, Burhans RC, Kent WJ, et al. (December 2006).
7912:
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7253:
7233:
7188:
7178:
7129:
7085:
7075:
7028:
6985:
6942:
6892:
6865:
6822:
6777:
6741:
6731:
6704:
6684:
6649:
6603:
6593:
6538:
6511:
6476:
6436:
6385:
6377:
6328:
6289:
6254:
6211:
6176:
6131:
6123:
6096:
6076:
6033:
5983:
5942:
5901:
5891:
5852:
5808:
5777:
5757:
5711:
5670:
5619:
5569:
5514:
5506:
5472:
5452:
5426:
5406:
5361:
5328:
5308:
5252:
5209:
5165:
5118:
5068:
5030:
4987:
4942:
4894:
4884:
4832:
4778:
4741:
4731:
4675:
4667:
4626:
4618:
4574:
4533:
4525:
4484:
4430:
4402:
4374:
4337:
4327:
4278:
4268:
4213:
4176:
4166:
4125:
4089:
4071:
4053:
3532:
3156:
2955:
289:
255:
163:
159:
95:
87:
63:
5510:
4563:"Chemical Paleogenetics. Molecular "Restoration Studies" of Extinct Forms of Life"
3405:
3325:
3163:
2801:
lizards show remarkable morphological diversity, including in the relative muscle
2720:. For criticism of ancestral reconstruction computation methods see Williams P.D.
9586:
9514:
7183:
4889:
4736:
4332:
4273:
4058:
3961:
2830:
2810:
2802:
2798:
1434:
300:
9172:
Patro R, Sefer E, Malin J, Marรงais G, Navlakha S, Kingsford C (September 2012).
9058:
8913:
7575:
7558:
1987:
between adjacent nodes given by some other continuous probability distribution.
1641:) by maximum likelihood, the procedure is: find the maximum likelihood estimate
9370:
Proceedings of the National Academy of Sciences of the United States of America
8281:
Proceedings of the National Academy of Sciences of the United States of America
8150:
7599:
7416:
Krishnan NM, Seligmann H, Stewart CB, De Koning AP, Pollock DD (October 2004).
7273:
Proceedings of the National Academy of Sciences of the United States of America
7060:
Proceedings of the National Academy of Sciences of the United States of America
6037:
4782:
4622:
4024:
3995:
3901:
3552:
3363:
TSV/CSV of species regions. Rows are species and columns are geographic regions
3095:
2767:
2681:
206:
118:
35:
9331:
9266:"FastML: a web server for probabilistic reconstruction of ancestral sequences"
8405:
8249:
8222:
8155:
Computer program and manual available by anonymous FTP from Uppsala University
8126:
8099:
8075:
8058:
7824:
7032:
6869:
6736:
6688:
6634:
Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution
6598:
6542:
6441:
6414:
6258:
5675:
5648:
5410:
4837:
4810:
4671:
4656:"Analyzing protein structure and function using ancestral gene reconstruction"
4489:
4462:
3272:
9618:
9315:"MLGO: phylogeny reconstruction and ancestral inference from gene-order data"
8870:
8819:
8352:
Yang Z (August 2007). "PAML 4: phylogenetic analysis by maximum likelihood".
7762:
7702:"Genome-scale evolution: reconstructing gene orders in the ancestral species"
6301:
6112:"Robustness of ancestral sequence reconstruction to phylogenetic uncertainty"
5723:
5633:
5464:
5373:
5264:
5177:
5080:
5042:
4954:
4588:
4386:
4225:
4139:
4067:
2814:
875:
uses the likelihood of observed data to update the investigator's belief, or
167:
155:
109:
39:
9400:
8758:
8708:
8502:
8375:
8057:
Clark JR, Ree RH, Alfaro ME, King MG, Wagner WL, Roalson EH (October 2008).
7916:
7602:, Rodrigo AG, Nickle DC, Li F, Mahalanabis M, et al. (September 2005).
7478:
7434:
7417:
7293:
7267:
Sadqi M, de Alba E, Pรฉrez-Jimรฉnez R, Sanchez-Ruiz JM, Muรฑoz V (March 2009).
7134:
7080:
6180:
6127:
5896:
5879:
5624:
5607:
5495:"A new method of inference of ancestral nucleotide and amino acid sequences"
5365:
4130:
4113:
3946:
variation. MLGO is a web-server for maximum likelihood gene order analysis.
3068:
Phylogeny of 7 regional strains of Drosophila pseudoobscura, as inferred by
9605:
9533:
9419:
9350:
9299:
9250:
9209:
9190:
9158:
9107:
9066:
9023:
8974:
8921:
8862:
8776:
8727:
8661:
8642:
8610:
8561:
8520:
8453:
8383:
8320:
8258:
8194:
8135:
8084:
8038:
7981:
7924:
7881:
7832:
7727:
7686:
7637:
7584:
7543:
7486:
7443:
7402:
7353:
7312:
7202:
7143:
6989:
6962:
6904:
6834:
6799:
6755:
6696:
6661:
6617:
6450:
6399:
6381:
6342:
6266:
6223:
6145:
6088:
6045:
5956:
5915:
5864:
5684:
5418:
5320:
5229:
5132:
4908:
4846:
4790:
4755:
4689:
4640:
4547:
4498:
4442:
4394:
4351:
4292:
4190:
4171:
4085:
3700:
3580:
3218:
3032:
3001:
2780:
1441:. Using this model as the basis for statistical inference, one can now use
1426:
1405:
422:
365:
9462:
9139:
8301:
8020:
7245:
7099:
7040:
6997:
6188:
5997:
5820:
5769:
5581:
5528:
4999:
4769:
Ronquist F (September 2004). "Bayesian inference of character evolution".
4093:
9281:
8592:
8398:"Lazarus: a software tool for reconstructing ancestral protein sequences"
7668:
7525:
5972:"PAML: a program package for phylogenetic analysis by maximum likelihood"
3830:
Custom text format for model parameters, tree, observed character values.
3559:
3116:
3020:
2935:
2880:
2826:
2771:
857:
304:
8626:"SIMMAP: stochastic character mapping of discrete traits on phylogenies"
7326:
Chang BS, Jรถnsson K, Kazmi MA, Donoghue MJ, Sakmar TP (September 2002).
6653:
3587:
2754:
Both phylogenetic and character data are available for the radiation of
2712:
Ancestral reconstruction allows for the study of evolutionary pathways,
1967:
9454:
8965:
7963:
7863:
6954:
5812:
5761:
5573:
5272:
5221:
5088:
4991:
4233:
3043:
3000:
strains sampled from twenty localities in Europe and Asia, and for 101
2867:
2743:
2738:
1430:
1413:
222:
172:
8485:
Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (December 2013).
7894:
7811:
Wienberg J (December 2004). "The evolution of eutherian chromosomes".
6896:
5906:
4529:
3840:
None specified, although site indicates software is freely available.
3662:
2793:
9550:, Trinh A, Sipos B, Brenton JD, Goldman N, Markowetz F (April 2014).
7651:
McCloskey RM, Liang RH, Harrigan PR, Brumme ZL, Poon AF (June 2014).
7266:
7237:
6415:"Estimating a binary character's effect on speciation and extinction"
6080:
3882:
3297:
3016:
3012:
2970:
2829:
species comparing stable models of continuous character evolution to
1957:
218:
134:
122:
113:
75:
43:
8469:"Mesquite: a modular system for evolutionary analysis. Version 2.75"
6946:
6674:
5256:
5213:
5169:
5072:
4712:"Assessing the accuracy of ancestral protein reconstruction methods"
4217:
4155:"Reconstruction of ancestral protein sequences and its applications"
9225:"Ancestors 1.0: a web server for ancestral sequence reconstruction"
6480:
5456:
4114:"The Assumptions and Challenges of Ancestral State Reconstructions"
3727:
Tab-delimited text file of rows for taxa and count data in columns.
3336:
TSV or space delimited table. Rows are species, columns are traits.
2912:
2786:
2775:
2573:, which describes the variance of the driving Brownian motion, and
1400:
1386:
rapidly becomes too vast, making it computationally infeasible for
198:
9568:
9382:
9263:
5401:
4710:
Williams PD, Pollock DD, Blackburne BP, Goldstein RA (June 2006).
4709:
4560:
4463:"Bayesian estimation of ancestral character states on phylogenies"
3507:
1119:
represents both the evolutionary model and the phylogenetic tree.
7845:
7559:"Ancestral and consensus envelope immunogens for HIV-1 subtype C"
7415:
6630:
6502:
Felsenstein J (1988). "Phylogenies and quantitative characters".
3939:
3909:
3455:
3104:
2963:
2916:
2891:
2806:
2733:
1994:
Plots of 200 trajectories of each of: Brownian motion with drift
202:
158:. Motivated by the development of techniques for determining the
67:
47:
8577:"PHAST and RPHAST: phylogenetic analysis with space/time models"
7269:"A designed protein as experimental model of primordial folding"
6109:
5443:
Felsenstein J (1985). "Phylogenies and the Comparative Method".
2653:, the process is less and less constrained by its attraction to
1603:{\displaystyle \mathbf {q} =\{q_{ij}:1\leq i,j\leq k,i\not =j\}}
1162:
is the likelihood of the observed data which can be computed by
338:
74:(e.g., gene order), a measurable characteristic of an organism (
8536:"MrBayes 3: Bayesian phylogenetic inference under mixed models"
3976:
2839:
1864:
1367:
71:
9640:
Knowledge articles published in peer-reviewed literature (J2W)
6110:
Hanson-Smith V, Kolaczkowski B, Thornton JW (September 2010).
4863:
Lemey P, Rambaut A, Drummond AJ, Suchard MA (September 2009).
3741:
9484:
Poon AF, Swenson LC, Bunnik EM, Edo-Matas D, Schuitemaker H,
8996:
Jones BR, Rajaraman A, Tannier E, Chauve C (September 2012).
8487:"MEGA6: Molecular Evolutionary Genetics Analysis version 6.0"
8484:
8468:
6528:
3943:
2876:
2755:
226:
150:
The concept of ancestral reconstruction is often credited to
7650:
7597:
7328:"Recreating a functional ancestral archosaur visual pigment"
7215:
7113:
Shapiro B, Rambaut A, Pybus OG, Holmes EC (September 2006).
7054:
Korber BT, Farber RM, Wolpert DH, Lapedes AS (August 1993).
6975:
5877:
4308:"Evolutionary history of hunter-gatherer marriage practices"
335:
than one possible state has been reconstructed at the root.
101:
Ancestral reconstruction relies on a sufficiently realistic
9552:"Phylogenetic quantification of intra-tumour heterogeneity"
8995:
8270:
8268:
7776:
Fertin G, Labarre A, Rusu I, Vialette S, Tannier E (2009).
7556:
6216:
10.1554/0014-3820(2000)054[0397:ICSWAR]2.0.CO;2
6103:
5841:
4862:
4607:"Inversions in the Chromosomes of Drosophila Pseudoobscura"
4600:
4598:
4022:
This article was adapted from the following source under a
3637:
2749:
1990:
1613:
9630:
Knowledge articles published in PLOS Computational Biology
9483:
9222:
8097:
7948:"Reconstructing contiguous regions of an ancestral genome"
7053:
6776:. Methods in Enzymology. Vol. 395. pp. 652โ670.
6009:
6007:
3191:
8741:
Drummond AJ, Suchard MA, Xie D, Rambaut A (August 2012).
8740:
7775:
7325:
7112:
7018:
5878:
Gruenheit N, Lockhart PJ, Steel M, Martin W (July 2008).
5199:
5146:
Sankoff D (1975). "Minimal Mutation Trees of Sequences".
4561:
Pauling L, Zuckerkandl E, Henriksen T, Lรถvstad R (1963).
4420:
4306:
Walker RS, Hill KR, Flinn MV, Ellsworth RM (April 2011).
3689:
2908:
2895:
1842:
model. In this model, all transitions have the same rate
1694:; then compute the likelihood of each possible state for
9625:
Knowledge articles published in peer-reviewed literature
9546:
9540:
9432:
8689:
8265:
8167:
Ree RH, Moore BR, Webb CO, Donoghue MJ (November 2005).
7994:
4924:
4595:
4305:
3793:
9357:
9120:
8843:
Proceedings of the Royal Society B: Biological Sciences
8527:
7456:
7012:
6004:
5922:
5286:
5284:
5282:
3908:(Bayesian Evolutionary Analysis by Sampling Trees) and
2969:
The reconstruction of ancestral genomes is also called
2774:" and those that consume vegetation are classified as "
2466:). Under this model, the above-described transition of
775:
is the branch length (evolutionary time) between nodes
254:
taxa (sequences) that descended from common ancestors.
9366:"Evolutionary inference via the Poisson Indel Process"
9223:
Diallo AB, Makarenkov V, Blanchette M (January 2010).
9171:
8743:"Bayesian phylogenetics with BEAUti and the BEAST 1.7"
8091:
7507:
7157:
Poon AF, Lewis FI, Pond SL, Frost SD (November 2007).
6158:
5290:
4705:
4703:
4701:
4699:
4554:
3924:
Genome rearrangements provide valuable information in
2727:
1938:
1909:
217:
Any attempt at ancestral reconstruction begins with a
205:, the geographic location of populations and species (
9216:
8683:
8173:
Evolution; International Journal of Organic Evolution
8098:
Huelsenbeck JP, Nielsen R, Bollback JP (April 2003).
7366:
6935:
Evolution; International Journal of Organic Evolution
6624:
6321:
Evolution; International Journal of Organic Evolution
6204:
Evolution; International Journal of Organic Evolution
5871:
5202:
Evolution; International Journal of Organic Evolution
4920:
4918:
3094:
Reconstructions of the words and phenomes of ancient
2942:(a segment of the permutation is reversed in-place),
2684:, one whose values at fixed times are distributed as
2659:
2639:
2619:
2599:
2579:
2552:
2532:
2512:
2492:
2472:
2452:
2415:
2385:
2365:
2345:
2325:
2305:
2285:
2265:
2245:
2225:
2205:
2185:
2148:
2115:
2086:
2053:
2020:
2000:
1968:
Example: Binary state speciation and extinction model
1932:
1903:
1881:
1848:
1824:
1802:
1762:
1720:
1700:
1678:
1647:
1627:
1536:
1515:
1483:
1463:
1341:
1308:
1287:
1267:
1209:
1172:
1125:
1105:
895:
809:
789:
751:
720:
453:
225:
about the order in which populations (referred to as
8734:
8480:
8478:
8274:
8166:
6882:
6195:
5279:
5195:
5193:
5191:
5189:
5187:
5014:
4604:
3972:
2593:, which describes the strength of its attraction to
9363:
8989:
8942:
8574:
8533:
8216:
8214:
8212:
6774:
Molecular Evolution: Producing the Biochemical Data
6567:
6565:
6563:
6561:
6412:
6406:
6279:
6013:
5931:"MRBAYES: Bayesian inference of phylogenetic trees"
5928:
5488:
5486:
5484:
5482:
4696:
4511:
3004:sequences sampled across twelve African countries.
2794:
Morphological and physiological character evolution
1457:Suppose the trait in question may fall into one of
1250:
9426:
9257:
9174:"Parsimonious reconstruction of network evolution"
8568:
8056:
7644:
7156:
6767:
6765:
6717:
6314:
6238:
5735:
5733:
5640:
5535:
5438:
5436:
4915:
4858:
4856:
4197:
3730:Count (numerical) data (e.g., homolog family size)
2665:
2645:
2625:
2605:
2585:
2565:
2538:
2518:
2498:
2478:
2458:
2428:
2401:
2371:
2351:
2331:
2311:
2291:
2271:
2251:
2231:
2211:
2191:
2163:
2134:
2101:
2072:
2039:
2006:
1947:
1918:
1887:
1854:
1830:
1808:
1783:
1746:{\displaystyle \mathbf {q} ={\hat {\mathbf {q} }}}
1745:
1706:
1686:
1664:
1633:
1602:
1521:
1501:
1469:
1347:
1323:
1293:
1273:
1232:
1195:
1154:
1111:
1081:
822:
795:
767:
733:
687:
9121:Carmel L, Wolf YI, Rogozin IB, Koonin EV (2010).
9036:
9030:
8475:
7769:
7734:
7693:
7501:
6413:Maddison WP, Midford PE, Otto SP (October 2007).
6357:
6315:Slater GJ, Harmon LJ, Alfaro ME (December 2012).
6273:
5184:
4647:
4505:
4299:
4240:
3889:package in the statistical computing environment
3861:program. In addition, LAZARUS is a collection of
2877:unweighted pair group method with arithmetic mean
2845:
9616:
8936:
8690:Rossnes R, Eidhammer I, Liberles DA (May 2005).
8575:Hubisz MJ, Pollard KS, Siepel A (January 2011).
8466:
8209:
8100:"Stochastic mapping of morphological characters"
7319:
7209:
7047:
6558:
6308:
6201:
6058:
6052:
5479:
5020:
4961:
4460:
4456:
4454:
4452:
2677:Stable models of continuous character evolution:
837:
46:relationships among individuals, populations or
9477:
9165:
9114:
8332:
8330:
8052:
8050:
8048:
7945:
7260:
6969:
6771:
6762:
5730:
5691:
5433:
5236:
4853:
4804:
4802:
4800:
4203:
3286:Qualitative and quantitative traits, Geographic
16:Extrapolation method to detect common ancestors
8998:"ANGES: reconstructing ANcestral GEnomeS maps"
8677:Analysis of Phylogenetics and Evolution with R
7699:
7360:
6711:
6668:
6462:
6460:
6244:
6152:
5784:
5646:
5541:
5341:
5095:
3410:Maximum Likelihood, Bayesian (as of version 2)
8885:
8783:
8617:
8428:"HyPhy: hypothesis testing using phylogenies"
8425:
8419:
7839:
7813:Current Opinion in Genetics & Development
7740:
7150:
6363:
5835:
4653:
4512:Sanger F, Thompson EO, Kitai R (March 1955).
4449:
4416:
4414:
4412:
4152:
698:where we are computing the likelihood of the
209:) and the higher-order structure of genomes.
121:and the concomitant development of efficient
8668:
8460:
8327:
8220:
8160:
8142:
8045:
7804:
7409:
6926:
6571:
5704:Computational Statistics & Data Analysis
5601:
5599:
5492:
5386:
5335:
5054:
5052:
4967:
4797:
4762:
4605:Dobzhansky T, Sturtevant AH (January 1938).
4107:
4105:
2770:", those that ingest arthropods are termed "
1597:
1545:
1433:"), the process is frequently taken to be a
1390:to converge in a reasonable amount of time.
9364:Bouchard-Cรดtรฉ A, Jordan MI (January 2013).
7939:
7550:
7450:
7106:
6501:
6457:
5790:
5739:
5697:
5442:
5380:
5242:
5139:
4461:Pagel M, Meade A, Barker D (October 2004).
4153:Cai W, Pei J, Grishin NV (September 2004).
3900:Several software packages also reconstruct
2409:In this case, there is only one parameter (
245:. Eventually, all lineages converge to the
9306:
9073:
8891:
8834:
8534:Ronquist F, Huelsenbeck JP (August 2003).
7888:
6911:
5929:Huelsenbeck JP, Ronquist F (August 2001).
5101:
4409:
3388:Fasta, NBRF, Genbank, PHYLIP, CLUSTAL, TSV
1981:
221:. In general, a phylogeny is a tree-based
9595:
9585:
9567:
9523:
9513:
9409:
9399:
9381:
9340:
9330:
9312:
9289:
9240:
9199:
9189:
9148:
9138:
9097:
9013:
8964:
8766:
8717:
8707:
8651:
8641:
8600:
8551:
8510:
8443:
8426:Pond SL, Frost SD, Muse SV (March 2005).
8365:
8310:
8300:
8275:Sturtevant AH, Dobzhansky T (July 1936).
8248:
8238:
8184:
8125:
8115:
8074:
8028:
7971:
7871:
7717:
7676:
7627:
7574:
7533:
7433:
7392:
7343:
7302:
7292:
7192:
7182:
7133:
7089:
7079:
6745:
6735:
6607:
6597:
6440:
6430:
6389:
6332:
6135:
6027:
5987:
5946:
5905:
5895:
5674:
5664:
5623:
5596:
5563:
5518:
5400:
5355:
5159:
5122:
5049:
4981:
4898:
4888:
4865:"Bayesian phylogeography finds its roots"
4836:
4826:
4745:
4735:
4679:
4630:
4578:
4537:
4488:
4478:
4358:
4341:
4331:
4282:
4272:
4249:"The phylogeny of Little Red Riding Hood"
4180:
4170:
4146:
4129:
4102:
4075:
4057:
3400:Creative Commons Attribution 3.0 License
3153:Continuous (C) or Discrete Characters (D)
2825:In an analysis of the body mass of 1,679
2359:is given by a Gaussian density with mean
1429:; for continuous-valued traits (such as "
212:
197:sequences, but also for the structure or
8789:
8623:
8345:
8341:. Edinburgh: Edinburgh University Press.
8336:
8148:
7810:
6932:
6855:
6504:Annual Review of Ecology and Systematics
5976:Computer Applications in the Biosciences
5963:
5493:Yang Z, Kumar S, Nei M (December 1995).
4808:
4768:
3876:
3851:
3063:
2928:
2873:three-dimensional structure of a protein
2750:Diet reconstruction in Galapagos finches
1989:
1956:
1863:
1756:Because such models may have as many as
1612:
1452:
337:
8674:
8339:Historical linguistics: an introduction
7788:10.7551/mitpress/9780262062824.001.0001
6466:
5145:
4246:
3846:
3089:
2985:
9617:
9079:
7779:Combinatorics of Genome Rearrangements
7700:Bourque G, Pevzner PA (January 2002).
6917:
6812:
6572:Elliot MG, Mooers Aร (November 2014).
4364:
4111:
3813:GNU General Public License, version 3
3788:GNU General Public License, version 3
3746:Maximum parsimony, maximum likelihood.
3372:GNU General Public License, version 2
3292:GNU General Public License, version 2
2861:
2820:
2697:
2446:selection around a certain value (say
2279:, the likelihood of a transition from
2259:) and separated by a branch of length
1099:corresponds to the observed data, and
50:to their ancestors. In the context of
42:, the reconstruction and study of the
9313:Hu F, Lin Y, Tang J (November 2014).
9039:Molecular Phylogenetics and Evolution
8894:Molecular Phylogenetics and Evolution
8840:
7345:10.1093/oxfordjournals.molbev.a004211
6364:Webster AJ, Purvis A (January 2002).
5647:Guindon S, Gascuel O (October 2003).
5605:
5058:
4660:Current Opinion in Structural Biology
4435:10.1093/oxfordjournals.molbev.a026369
3721:Maximum Parsimony, maximum likelihood
2858:related by non-overlapping branches.
2109:(green); and Ornstein-Uhlenbeck with
1665:{\displaystyle {\hat {\mathbf {q} }}}
867:
402:
119:exponential growth of computing power
8351:
8221:Lemmon AR, Lemmon EM (August 2008).
5969:
3949:
3346:Creative Commons Attribution License
3232:Qualitative and quantitative traits
2813:character evolution) indicates that
1818:: this model is the reverse-in-time
277:
201:properties of ancient versus modern
38:. It is an important application of
6885:The Journal of Experimental Biology
6718:Erkenbrack EM, Thompson JR (2019).
5148:SIAM Journal on Applied Mathematics
4654:Harms MJ, Thornton JW (June 2010).
3965:ancestral sequence reconstruction.
3932:
3339:Qualitative and quantitative traits
2728:Behavior and life history evolution
2219:are adjacent in the phylogeny (say
741:denotes the character state of the
13:
8186:10.1111/j.0014-3820.2005.tb00940.x
7620:10.1128/JVI.79.17.11214-11224.2005
4809:Ree RH, Smith SA (February 2008).
3938:identification and arrangement of
3311:Nucleotide, Protein (customizable)
1449:to estimate the ancestral states.
790:
615:
532:
485:
288:Parsimony, known colloquially as "
14:
9656:
9635:Externally peer reviewed articles
8467:Maddison WP, Maddison DR (2015).
5293:Trends in Ecology & Evolution
4771:Trends in Ecology & Evolution
4006:Ancestral sequence reconstruction
3212:GNU Lesser General Public License
3026:
2902:
2047:(black); Ornstein-Uhlenbeck with
1095:represents the ancestral states,
382:Variation in time among lineages.
60:ancestral sequence reconstruction
9178:Algorithms for Molecular Biology
8957:10.1111/j.1096-0031.2011.00353.x
8812:10.1111/j.2041-210X.2012.00234.x
8792:Methods in Ecology and Evolution
7385:10.1128/JB.185.18.5573-5584.2003
6827:10.1111/j.1420-9101.2004.00770.x
6516:10.1146/annurev.ecolsys.19.1.445
6370:Proceedings. Biological Sciences
6334:10.1111/j.1558-5646.2012.01723.x
6294:10.1111/j.1463-6395.2008.00364.x
5857:10.1093/bioinformatics/18.8.1116
4970:Bulletin of Mathematical Biology
4580:10.3891/acta.chem.scand.17s-0009
4016:
3975:
2851:Phylogenetic comparative methods
1733:
1722:
1680:
1652:
1538:
1251:Empirical and hierarchical Bayes
357:Variation in rates of evolution.
9276:(Web Server issue): W580โW584.
8747:Molecular Biology and Evolution
8491:Molecular Biology and Evolution
8390:
8354:Molecular Biology and Evolution
7988:
7591:
7422:Molecular Biology and Evolution
7332:Molecular Biology and Evolution
7122:Molecular Biology and Evolution
6876:
6849:
6815:Journal of Evolutionary Biology
6806:
6677:Development Genes and Evolution
6549:
6522:
6495:
6116:Molecular Biology and Evolution
5989:10.1093/bioinformatics/13.5.555
5948:10.1093/bioinformatics/17.8.754
5884:Molecular Biology and Evolution
4423:Molecular Biology and Evolution
3205:Nucleotide, Protein, Geographic
2692:
1164:Felsenstein's pruning algorithm
9435:Journal of Molecular Evolution
5793:Journal of Molecular Evolution
5742:Journal of Molecular Evolution
5544:Journal of Molecular Evolution
5102:Stamatakis A (November 2006).
4927:Journal of Theoretical Biology
3496:Nucleotide, qualitative traits
3318:GNU Free Documentation License
2846:Correlated character evolution
2805:composition in their hindlimb
1948:{\displaystyle q_{\mbox{dec}}}
1919:{\displaystyle q_{\mbox{inc}}}
1778:
1766:
1737:
1656:
1393:
1318:
1312:
1227:
1220:
1213:
1190:
1183:
1176:
1155:{\displaystyle P(D|S,\theta )}
1149:
1136:
1129:
1072:
1066:
1060:
1053:
1046:
1040:
1027:
1020:
1001:
994:
987:
979:
972:
965:
959:
946:
939:
923:
910:
903:
667:
637:
623:
584:
554:
540:
506:
493:
364:tend to occur more often than
1:
9242:10.1093/bioinformatics/btp600
9099:10.1093/bioinformatics/btq315
9015:10.1093/bioinformatics/bts457
8624:Bollback JP (February 2006).
8553:10.1093/bioinformatics/btg180
8445:10.1093/bioinformatics/bti079
6782:10.1016/S0076-6879(05)95034-9
5716:10.1016/S0167-9473(02)00212-8
5313:10.1016/S0169-5347(98)01382-2
5124:10.1093/bioinformatics/btl446
4514:"The amide groups of insulin"
4379:10.1016/S0376-6357(99)00038-8
4011:
3382:Parsimony, Maximum Likelihood
2135:{\displaystyle \sigma ^{2}=1}
2073:{\displaystyle \sigma ^{2}=1}
2040:{\displaystyle \sigma ^{2}=1}
1372:Metropolis-Hastings algorithm
838:Marginal and joint likelihood
160:primary (amino acid) sequence
9587:10.1371/journal.pcbi.1003535
9515:10.1371/journal.pcbi.1002753
8679:. New York: Springer-Verlag.
7755:10.1016/0196-6774(81)90029-8
7184:10.1371/journal.pcbi.0030231
5035:10.1016/0025-5564(87)90074-5
4947:10.1016/0022-5193(82)90384-8
4890:10.1371/journal.pcbi.1000520
4737:10.1371/journal.pcbi.0020069
4333:10.1371/journal.pone.0019066
4274:10.1371/journal.pone.0078871
4059:10.1371/JOURNAL.PCBI.1004763
3918:continuous time Markov model
3592:Maximum Likelihood, Bayesian
3419:Geographic, Ecological niche
2990:
2909:human immunodeficiency virus
2402:{\displaystyle \sigma ^{2}t}
1687:{\displaystyle \mathbf {q} }
1331:over all possible values of
1233:{\displaystyle P(D|\theta )}
1196:{\displaystyle P(S|\theta )}
112:to determine the route that
7:
9059:10.1016/j.ympev.2005.03.026
8914:10.1016/j.ympev.2010.04.011
8581:Briefings in Bioinformatics
7576:10.1016/j.virol.2006.05.011
5698:Doornik JA, Ooms M (2003).
5511:10.1093/genetics/141.4.1641
3983:Evolutionary biology portal
3968:
3527:GNU General Public License
3122:
3051:relative to other methods.
2566:{\displaystyle \sigma ^{2}}
2429:{\displaystyle \sigma ^{2}}
2164:{\displaystyle \alpha =-40}
1502:{\displaystyle 1,\ldots ,k}
247:most recent common ancestor
10:
9661:
9556:PLOS Computational Biology
9494:PLOS Computational Biology
9127:Advances in Bioinformatics
7163:PLOS Computational Biology
6922:. Oxford: Clarendon Press.
6038:10.1080/106351501300317978
4869:PLOS Computational Biology
4783:10.1016/j.tree.2004.07.002
4716:PLOS Computational Biology
4045:PLOS Computational Biology
4040:"Ancestral Reconstruction"
3957:next-generation sequencing
3308:MEGA, NEXUS, FASTA, PHYLIP
3266:GNU General Public License
3239:GNU General Public License
3184:GNU General Public License
3117:nasal and non-nasal vowels
2440:Ornstein-Uhlenbeck process
2102:{\displaystyle \alpha =-4}
1838:-state counterpart of the
1439:Ornstein-Uhlenbeck process
412:genetic sequence evolution
389:Statistical justification.
281:
145:
9332:10.1186/s12859-014-0354-6
8250:10.1080/10635150802304761
8127:10.1080/10635150390192780
8076:10.1080/10635150802426473
7825:10.1016/j.gde.2004.10.001
6737:10.1038/s42003-019-0417-3
6689:10.1007/s00427-015-0527-y
6599:10.1186/s12862-014-0226-8
6442:10.1080/10635150701607033
6259:10.1080/10635150500541698
5676:10.1080/10635150390235520
5411:10.1080/10635150802203898
4838:10.1080/10635150701883881
4672:10.1016/j.sbi.2010.03.005
4567:Acta Chemica Scandinavica
4490:10.1080/10635150490522232
2179:: in this case, if nodes
1419:
440:along a branch of length
9080:Csurรถs M (August 2010).
6578:BMC Evolutionary Biology
5023:Mathematical Biosciences
4623:10.1093/genetics/23.1.28
4159:BMC Evolutionary Biology
3826:Win, Unix, Matlab module
2960:horizontal gene transfer
2946:(a segment is removed),
2907:RNA viruses such as the
2703:Ancestral reconstruction
1895:-state 2 parameter model
1816:-state 1 parameter model
1425:typically taken to be a
1364:Markov chain Monte Carlo
706:with direct descendants
190:Drosophila pseudoobscura
129:algorithm for the joint
123:computational algorithms
20:Ancestral reconstruction
9401:10.1073/pnas.1220450110
8709:10.1186/1471-2105-6-127
7917:10.1126/science.1111387
7479:10.1126/science.1070441
7373:Journal of Bacteriology
7294:10.1073/pnas.0812108106
7081:10.1073/pnas.90.15.7176
7033:10.1093/protein/7.3.349
6870:10.1093/sysbio/40.3.304
6543:10.1093/sysbio/42.3.265
6181:10.1126/science.1736360
5970:Yang Z (October 1997).
5625:10.1080/106351599260184
5445:The American Naturalist
5366:10.1080/106351599260193
4518:The Biochemical Journal
4131:10.1080/106351599260175
2626:{\displaystyle \alpha }
2586:{\displaystyle \alpha }
1982:Continuous-state models
1707:{\displaystyle \alpha }
1634:{\displaystyle \alpha }
1359:Empirical Bayes methods
1348:{\displaystyle \theta }
1294:{\displaystyle \theta }
1274:{\displaystyle \theta }
1112:{\displaystyle \theta }
849:computationally complex
845:marginal reconstruction
796:{\displaystyle \Omega }
307:. The first stage is a
70:, the composition of a
9488:, Harrigan PR (2012).
9270:Nucleic Acids Research
9191:10.1186/1748-7188-7-25
8863:10.1098/rspb.1994.0006
8643:10.1186/1471-2105-7-88
6990:10.1002/prot.340180402
6724:Communications Biology
6382:10.1098/rspb.2001.1873
4172:10.1186/1471-2148-4-33
3705:Gene order permutation
3678:Gene order permutation
3130:free software licenses
3077:
2998:Avian influenza A-H5N1
2866:On a molecular level,
2667:
2647:
2627:
2607:
2587:
2567:
2540:
2520:
2500:
2480:
2460:
2430:
2403:
2373:
2353:
2333:
2313:
2293:
2273:
2253:
2233:
2213:
2193:
2172:
2165:
2136:
2103:
2074:
2041:
2008:
1962:
1949:
1920:
1889:
1870:
1856:
1832:
1810:
1785:
1784:{\displaystyle k(k-1)}
1747:
1708:
1688:
1666:
1635:
1618:
1604:
1523:
1503:
1471:
1349:
1325:
1295:
1275:
1258:empirical Bayes method
1234:
1197:
1156:
1113:
1083:
881:posterior distribution
824:
797:
769:
768:{\displaystyle t_{ij}}
735:
689:
344:
213:Methods and algorithms
185:chromosomal inversions
31:Character Optimization
8759:10.1093/molbev/mss075
8503:10.1093/molbev/mst197
8376:10.1093/molbev/msm088
8302:10.1073/pnas.22.7.448
8021:10.1038/ismej.2016.67
7743:Journal of Algorithms
7435:10.1093/molbev/msh198
7135:10.1093/molbev/msl037
6128:10.1093/molbev/msq081
5897:10.1093/molbev/msn098
4367:Behavioural Processes
3877:Other character types
3632:GPL Creative Commons
3391:Nucleotide, Protein,
3256:NEXUS, FASTA, CLUSTAL
3067:
3031:Inferring historical
2929:Genome rearrangements
2668:
2648:
2628:
2608:
2588:
2568:
2541:
2521:
2501:
2481:
2461:
2431:
2404:
2374:
2354:
2334:
2314:
2294:
2274:
2254:
2234:
2214:
2194:
2166:
2137:
2104:
2075:
2042:
2009:
1993:
1975:diversification rates
1960:
1950:
1921:
1890:
1867:
1857:
1833:
1811:
1786:
1748:
1709:
1689:
1667:
1636:
1616:
1605:
1524:
1504:
1472:
1453:Discrete-state models
1350:
1326:
1296:
1276:
1235:
1198:
1157:
1114:
1084:
825:
823:{\displaystyle S_{x}}
798:
770:
736:
734:{\displaystyle S_{i}}
690:
395:Convergent evolution.
341:
177:Theodosius Dobzhansky
9645:Evolutionary biology
7669:10.1128/JVI.00483-14
7526:10.1128/JVI.02683-06
6891:(Pt 23): 4529โ4547.
3991:Evolutionary biology
3926:comparative genomics
3885:). For example, the
3847:Package descriptions
3174:PHYLIP, NEXUS, FASTA
3090:Linguistic Evolution
3044:dispersal-vicariance
2986:Spatial applications
2976:comparative genomics
2784:) and ground finch (
2686:stable distributions
2657:
2637:
2617:
2597:
2577:
2550:
2530:
2510:
2490:
2470:
2450:
2413:
2383:
2363:
2343:
2323:
2303:
2283:
2263:
2243:
2223:
2203:
2183:
2146:
2113:
2084:
2051:
2018:
1998:
1930:
1901:
1879:
1875:Asymmetrical Markov
1846:
1822:
1800:
1760:
1718:
1698:
1676:
1645:
1625:
1534:
1513:
1481:
1461:
1414:caniform carnivorans
1370:). For example, the
1339:
1324:{\displaystyle P(D)}
1306:
1285:
1265:
1207:
1170:
1123:
1103:
893:
807:
787:
749:
718:
451:
309:post-order traversal
52:evolutionary biology
9578:2014PLSCB..10E3535S
9506:2012PLSCB...8E2753P
9447:1991JMolE..33..114T
9392:2013PNAS..110.1160B
9140:10.1155/2010/167408
9051:2005MolPE..36..214L
8906:2010MolPE..56..848Y
8855:1994RSPSB.255...37P
8804:2012MEcEv...3.1084F
8337:Campbell L (1998).
8293:1936PNAS...22..448S
8149:Ronquist F (1996).
8013:2016ISMEJ..10.2931O
7909:2005Sci...309..613M
7657:Journal of Virology
7614:(17): 11214โ11224.
7608:Journal of Virology
7514:Journal of Virology
7471:2002Sci...296.2354G
7465:(5577): 2354โ2360.
7285:2009PNAS..106.4127S
7230:1995Natur.374...57J
7175:2007PLSCB...3..231P
7072:1993PNAS...90.7176K
7021:Protein Engineering
6654:10.1002/jez.b.22614
6646:2015JEZB..324..493G
6590:2014BMCEE..14..226E
6469:American Naturalist
6173:1992Sci...255..589H
6073:2001Natur.411..937L
5805:1998JMolE..47..686E
5754:1981JMolE..17..368F
5556:1996JMolE..42..313K
5305:1998TEcoE..13..361C
4939:1982JThBi..99....1W
4881:2009PLSCB...5E0520L
4728:2006PLSCB...2...69W
4573:(suplement): 9โ16.
4324:2011PLoSO...619066W
4265:2013PLoSO...878871T
4247:Tehrani JJ (2013).
3852:Molecular evolution
3823:Maximum likelihood.
3755:Nucleotide, Protein
3651:Nucleotide, Protein
3546:Biological networks
3521:Nucleotide, Protein
3444:Nucleotide (indels)
3259:Nucleotide, Protein
3223:Maximum Likelihood
3177:Nucleotide, Protein
3100:Proto-Indo-European
3058:Pseudacris feriarum
2868:amino acid residues
2862:Molecular evolution
2821:Mammalian body mass
2698:Character evolution
2239:is the ancestor of
332:pre-order traversal
127:dynamic programming
64:amino acid sequence
9455:10.1007/BF02193625
9319:BMC Bioinformatics
9282:10.1093/nar/gks498
8696:BMC Bioinformatics
8675:Paradis E (2012).
8630:BMC Bioinformatics
8593:10.1093/bib/bbq072
8402:markov.uoregon.edu
8227:Systematic Biology
8151:"DIVA version 1.1"
8104:Systematic Biology
8063:Systematic Biology
7964:10.1101/gr.5383506
7864:10.1101/gr.3955206
6858:Systematic Biology
6531:Systematic Biology
6419:Systematic Biology
6247:Systematic Biology
6016:Systematic Biology
5813:10.1007/PL00006427
5762:10.1007/BF01734359
5653:Systematic Biology
5612:Systematic Biology
5574:10.1007/BF02198858
5389:Systematic Biology
5344:Systematic Biology
5245:Systematic Zoology
5061:Systematic Zoology
4992:10.1007/BF02459467
4815:Systematic Biology
4467:Systematic Biology
4206:Systematic Zoology
4118:Systematic Biology
4112:Omland KE (1999).
4001:Enzyme promiscuity
3798:Maximum Likelihood
3711:GNU GPL version 2
3667:Maximum likelihood
3642:Maximum Likelihood
3571:Multiple Alignment
3565:Maximum Likelihood
3485:Stochastic Mapping
3435:Maximum Likelihood
3357:Maximum Likelihood
3302:Maximum Likelihood
3277:Maximum Likelihood
3250:Maximum Likelihood
3168:Maximum Likelihood
3113:sequence alignment
3078:
2714:adaptive selection
2663:
2643:
2623:
2603:
2583:
2563:
2536:
2516:
2496:
2476:
2456:
2426:
2399:
2369:
2349:
2329:
2309:
2289:
2269:
2249:
2229:
2209:
2189:
2173:
2161:
2132:
2099:
2070:
2037:
2004:
1963:
1945:
1942:
1916:
1913:
1885:
1871:
1852:
1828:
1806:
1781:
1743:
1704:
1684:
1662:
1631:
1619:
1600:
1519:
1499:
1467:
1447:Bayesian inference
1443:maximum likelihood
1384:all possible trees
1345:
1321:
1291:
1271:
1230:
1193:
1152:
1109:
1079:
1077:
877:prior distribution
873:Bayesian inference
868:Bayesian inference
820:
793:
765:
731:
685:
619:
536:
489:
408:Maximum likelihood
403:Maximum likelihood
345:
272:Bayesian Inference
268:maximum likelihood
131:maximum likelihood
106:model of evolution
84:phylogenetic trees
9092:(15): 1910โ1912.
9008:(18): 2388โ2390.
8546:(12): 1572โ1574.
8497:(12): 2725โ2729.
8179:(11): 2299โ2311.
8007:(12): 2931โ2945.
7958:(12): 1557โ1565.
7903:(5734): 613โ617.
7663:(11): 6181โ6194.
7520:(16): 8507โ8514.
7428:(10): 1871โ1883.
7379:(18): 5573โ5584.
7279:(11): 4127โ4132.
7066:(15): 7176โ7180.
6918:Ridley M (1983).
6897:10.1242/jeb.01903
6376:(1487): 143โ149.
6327:(12): 3931โ3944.
6167:(5044): 589โ592.
6067:(6840): 937โ940.
5117:(21): 2688โ2690.
4530:10.1042/bj0590509
3950:Future directions
3844:
3843:
3617:Maximum Parsimony
3537:Maximum Parsimony
3460:Maximum Parsimony
3150:! Character Types
2764:Galapagos finches
2760:Galapagos Islands
2666:{\displaystyle 0}
2646:{\displaystyle 0}
2606:{\displaystyle 0}
2539:{\displaystyle y}
2519:{\displaystyle V}
2499:{\displaystyle x}
2479:{\displaystyle U}
2459:{\displaystyle 0}
2372:{\displaystyle 0}
2352:{\displaystyle y}
2332:{\displaystyle V}
2312:{\displaystyle x}
2292:{\displaystyle U}
2272:{\displaystyle t}
2252:{\displaystyle V}
2232:{\displaystyle U}
2212:{\displaystyle V}
2192:{\displaystyle U}
2007:{\displaystyle 0}
1941:
1912:
1888:{\displaystyle k}
1855:{\displaystyle q}
1831:{\displaystyle k}
1809:{\displaystyle k}
1740:
1659:
1522:{\displaystyle k}
1477:states, labelled
1470:{\displaystyle k}
1005:
597:
514:
467:
294:maximum parsimony
284:Maximum Parsimony
278:Maximum parsimony
264:maximum parsimony
181:Alfred Sturtevant
152:Emile Zuckerkandl
135:phylogenetic tree
96:ancient languages
88:genetic sequences
25:Character Mapping
9652:
9610:
9609:
9599:
9589:
9571:
9544:
9538:
9537:
9527:
9517:
9500:(11): e1002753.
9481:
9475:
9474:
9430:
9424:
9423:
9413:
9403:
9385:
9376:(4): 1160โ1166.
9361:
9355:
9354:
9344:
9334:
9310:
9304:
9303:
9293:
9261:
9255:
9254:
9244:
9220:
9214:
9213:
9203:
9193:
9169:
9163:
9162:
9152:
9142:
9118:
9112:
9111:
9101:
9077:
9071:
9070:
9034:
9028:
9027:
9017:
8993:
8987:
8986:
8968:
8940:
8934:
8933:
8889:
8883:
8882:
8838:
8832:
8831:
8798:(6): 1084โ1092.
8787:
8781:
8780:
8770:
8753:(8): 1969โ1973.
8738:
8732:
8731:
8721:
8711:
8687:
8681:
8680:
8672:
8666:
8665:
8655:
8645:
8621:
8615:
8614:
8604:
8572:
8566:
8565:
8555:
8531:
8525:
8524:
8514:
8482:
8473:
8472:
8464:
8458:
8457:
8447:
8423:
8417:
8416:
8414:
8413:
8404:. Archived from
8394:
8388:
8387:
8369:
8360:(8): 1586โ1591.
8349:
8343:
8342:
8334:
8325:
8324:
8314:
8304:
8272:
8263:
8262:
8252:
8242:
8218:
8207:
8206:
8188:
8164:
8158:
8157:
8146:
8140:
8139:
8129:
8119:
8095:
8089:
8088:
8078:
8054:
8043:
8042:
8032:
8001:The ISME Journal
7992:
7986:
7985:
7975:
7943:
7937:
7936:
7892:
7886:
7885:
7875:
7843:
7837:
7836:
7808:
7802:
7801:
7773:
7767:
7766:
7738:
7732:
7731:
7721:
7697:
7691:
7690:
7680:
7648:
7642:
7641:
7631:
7595:
7589:
7588:
7578:
7554:
7548:
7547:
7537:
7505:
7499:
7498:
7454:
7448:
7447:
7437:
7413:
7407:
7406:
7396:
7364:
7358:
7357:
7347:
7338:(9): 1483โ1489.
7323:
7317:
7316:
7306:
7296:
7264:
7258:
7257:
7238:10.1038/374057a0
7213:
7207:
7206:
7196:
7186:
7154:
7148:
7147:
7137:
7128:(9): 1724โ1730.
7119:
7110:
7104:
7103:
7093:
7083:
7051:
7045:
7044:
7016:
7010:
7009:
6973:
6967:
6966:
6930:
6924:
6923:
6915:
6909:
6908:
6880:
6874:
6873:
6853:
6847:
6846:
6821:(6): 1230โ1237.
6810:
6804:
6803:
6769:
6760:
6759:
6749:
6739:
6715:
6709:
6708:
6672:
6666:
6665:
6628:
6622:
6621:
6611:
6601:
6569:
6556:
6553:
6547:
6546:
6526:
6520:
6519:
6499:
6493:
6492:
6464:
6455:
6454:
6444:
6434:
6410:
6404:
6403:
6393:
6361:
6355:
6354:
6336:
6312:
6306:
6305:
6277:
6271:
6270:
6242:
6236:
6235:
6199:
6193:
6192:
6156:
6150:
6149:
6139:
6122:(9): 1988โ1999.
6107:
6101:
6100:
6081:10.1038/35082053
6056:
6050:
6049:
6031:
6011:
6002:
6001:
5991:
5967:
5961:
5960:
5950:
5926:
5920:
5919:
5909:
5899:
5890:(7): 1512โ1520.
5875:
5869:
5868:
5851:(8): 1116โ1123.
5839:
5833:
5832:
5788:
5782:
5781:
5737:
5728:
5727:
5695:
5689:
5688:
5678:
5668:
5644:
5638:
5637:
5627:
5606:Pagel M (1999).
5603:
5594:
5593:
5567:
5565:10.1.1.1031.2646
5539:
5533:
5532:
5522:
5505:(4): 1641โ1650.
5490:
5477:
5476:
5440:
5431:
5430:
5404:
5384:
5378:
5377:
5359:
5339:
5333:
5332:
5288:
5277:
5276:
5240:
5234:
5233:
5208:(6): 1699โ1711.
5197:
5182:
5181:
5163:
5143:
5137:
5136:
5126:
5108:
5099:
5093:
5092:
5056:
5047:
5046:
5018:
5012:
5011:
4985:
4965:
4959:
4958:
4922:
4913:
4912:
4902:
4892:
4860:
4851:
4850:
4840:
4830:
4806:
4795:
4794:
4766:
4760:
4759:
4749:
4739:
4707:
4694:
4693:
4683:
4651:
4645:
4644:
4634:
4602:
4593:
4592:
4582:
4558:
4552:
4551:
4541:
4509:
4503:
4502:
4492:
4482:
4458:
4447:
4446:
4418:
4407:
4406:
4362:
4356:
4355:
4345:
4335:
4303:
4297:
4296:
4286:
4276:
4244:
4238:
4237:
4201:
4195:
4194:
4184:
4174:
4150:
4144:
4143:
4133:
4109:
4098:
4097:
4079:
4061:
4034:reviewer reports
4027:
4020:
3985:
3980:
3979:
3933:Web applications
3202:NEXUS, BEAST XML
3157:Software License
3135:
3134:
2827:placental mammal
2672:
2670:
2669:
2664:
2652:
2650:
2649:
2644:
2632:
2630:
2629:
2624:
2612:
2610:
2609:
2604:
2592:
2590:
2589:
2584:
2572:
2570:
2569:
2564:
2562:
2561:
2545:
2543:
2542:
2537:
2525:
2523:
2522:
2517:
2505:
2503:
2502:
2497:
2485:
2483:
2482:
2477:
2465:
2463:
2462:
2457:
2435:
2433:
2432:
2427:
2425:
2424:
2408:
2406:
2405:
2400:
2395:
2394:
2378:
2376:
2375:
2370:
2358:
2356:
2355:
2350:
2338:
2336:
2335:
2330:
2318:
2316:
2315:
2310:
2298:
2296:
2295:
2290:
2278:
2276:
2275:
2270:
2258:
2256:
2255:
2250:
2238:
2236:
2235:
2230:
2218:
2216:
2215:
2210:
2198:
2196:
2195:
2190:
2170:
2168:
2167:
2162:
2141:
2139:
2138:
2133:
2125:
2124:
2108:
2106:
2105:
2100:
2079:
2077:
2076:
2071:
2063:
2062:
2046:
2044:
2043:
2038:
2030:
2029:
2013:
2011:
2010:
2005:
1954:
1952:
1951:
1946:
1944:
1943:
1939:
1925:
1923:
1922:
1917:
1915:
1914:
1910:
1894:
1892:
1891:
1886:
1861:
1859:
1858:
1853:
1837:
1835:
1834:
1829:
1815:
1813:
1812:
1807:
1790:
1788:
1787:
1782:
1752:
1750:
1749:
1744:
1742:
1741:
1736:
1731:
1725:
1714:conditioning on
1713:
1711:
1710:
1705:
1693:
1691:
1690:
1685:
1683:
1671:
1669:
1668:
1663:
1661:
1660:
1655:
1650:
1640:
1638:
1637:
1632:
1609:
1607:
1606:
1601:
1560:
1559:
1541:
1528:
1526:
1525:
1520:
1508:
1506:
1505:
1500:
1476:
1474:
1473:
1468:
1401:bacteriophage T7
1354:
1352:
1351:
1346:
1330:
1328:
1327:
1322:
1300:
1298:
1297:
1292:
1280:
1278:
1277:
1272:
1239:
1237:
1236:
1231:
1223:
1202:
1200:
1199:
1194:
1186:
1166:as given above.
1161:
1159:
1158:
1153:
1139:
1118:
1116:
1115:
1110:
1088:
1086:
1085:
1080:
1078:
1056:
1030:
1010:
1006:
1004:
997:
982:
975:
949:
934:
913:
829:
827:
826:
821:
819:
818:
802:
800:
799:
794:
774:
772:
771:
766:
764:
763:
740:
738:
737:
732:
730:
729:
694:
692:
691:
686:
684:
680:
679:
678:
666:
665:
650:
649:
640:
635:
634:
618:
611:
610:
596:
595:
583:
582:
567:
566:
557:
552:
551:
535:
528:
527:
505:
504:
488:
481:
480:
463:
462:
372:Rapid evolution.
324:set intersection
164:Frederick Sanger
80:geographic range
56:genetic sequence
36:common ancestors
9660:
9659:
9655:
9654:
9653:
9651:
9650:
9649:
9615:
9614:
9613:
9562:(4): e1003535.
9545:
9541:
9482:
9478:
9431:
9427:
9362:
9358:
9311:
9307:
9262:
9258:
9221:
9217:
9170:
9166:
9119:
9115:
9078:
9074:
9035:
9031:
8994:
8990:
8941:
8937:
8890:
8886:
8849:(1342): 37โ45.
8839:
8835:
8788:
8784:
8739:
8735:
8688:
8684:
8673:
8669:
8622:
8618:
8573:
8569:
8532:
8528:
8483:
8476:
8465:
8461:
8424:
8420:
8411:
8409:
8396:
8395:
8391:
8367:10.1.1.322.1650
8350:
8346:
8335:
8328:
8273:
8266:
8240:10.1.1.585.7211
8219:
8210:
8165:
8161:
8147:
8143:
8117:10.1.1.386.9241
8096:
8092:
8055:
8046:
7993:
7989:
7952:Genome Research
7944:
7940:
7893:
7889:
7852:Genome Research
7844:
7840:
7809:
7805:
7798:
7774:
7770:
7739:
7735:
7706:Genome Research
7698:
7694:
7649:
7645:
7598:Doria-Rose NA,
7596:
7592:
7555:
7551:
7506:
7502:
7455:
7451:
7414:
7410:
7365:
7361:
7324:
7320:
7265:
7261:
7224:(6517): 57โ59.
7214:
7210:
7155:
7151:
7117:
7111:
7107:
7052:
7048:
7017:
7013:
6974:
6970:
6947:10.2307/2409434
6931:
6927:
6916:
6912:
6881:
6877:
6854:
6850:
6811:
6807:
6792:
6770:
6763:
6716:
6712:
6673:
6669:
6629:
6625:
6570:
6559:
6554:
6550:
6527:
6523:
6500:
6496:
6465:
6458:
6432:10.1.1.150.2224
6411:
6407:
6362:
6358:
6313:
6309:
6278:
6274:
6243:
6239:
6200:
6196:
6157:
6153:
6108:
6104:
6057:
6053:
6029:10.1.1.319.4271
6012:
6005:
5968:
5964:
5927:
5923:
5876:
5872:
5840:
5836:
5789:
5785:
5738:
5731:
5696:
5692:
5666:10.1.1.110.5852
5645:
5641:
5604:
5597:
5540:
5536:
5491:
5480:
5441:
5434:
5385:
5381:
5340:
5336:
5289:
5280:
5257:10.2307/2412304
5241:
5237:
5214:10.2307/2410994
5198:
5185:
5170:10.1137/0128004
5161:10.1.1.665.9596
5144:
5140:
5106:
5100:
5096:
5073:10.2307/2412116
5057:
5050:
5019:
5015:
4966:
4962:
4923:
4916:
4875:(9): e1000520.
4861:
4854:
4828:10.1.1.457.2776
4807:
4798:
4767:
4763:
4708:
4697:
4652:
4648:
4603:
4596:
4559:
4555:
4510:
4506:
4480:10.1.1.483.4931
4459:
4450:
4419:
4410:
4363:
4359:
4304:
4300:
4245:
4241:
4218:10.2307/2412794
4202:
4198:
4151:
4147:
4110:
4103:
4052:(7): e1004763.
4037:
4023:
4021:
4014:
3981:
3974:
3971:
3962:"deep" snapshot
3952:
3935:
3879:
3854:
3849:
3771:Local Parsimony
3492:XML-like format
3469:Gene expression
3360:Linux, Mac, Win
3226:Unix, Mac, Win
3125:
3096:proto-languages
3092:
3029:
2993:
2988:
2931:
2905:
2864:
2848:
2831:Brownian motion
2823:
2811:Brownian motion
2796:
2758:inhabiting the
2752:
2730:
2700:
2695:
2658:
2655:
2654:
2638:
2635:
2634:
2618:
2615:
2614:
2598:
2595:
2594:
2578:
2575:
2574:
2557:
2553:
2551:
2548:
2547:
2531:
2528:
2527:
2526:being in state
2511:
2508:
2507:
2491:
2488:
2487:
2486:being in state
2471:
2468:
2467:
2451:
2448:
2447:
2420:
2416:
2414:
2411:
2410:
2390:
2386:
2384:
2381:
2380:
2364:
2361:
2360:
2344:
2341:
2340:
2339:being in state
2324:
2321:
2320:
2304:
2301:
2300:
2299:being in state
2284:
2281:
2280:
2264:
2261:
2260:
2244:
2241:
2240:
2224:
2221:
2220:
2204:
2201:
2200:
2184:
2181:
2180:
2177:Brownian motion
2147:
2144:
2143:
2120:
2116:
2114:
2111:
2110:
2085:
2082:
2081:
2058:
2054:
2052:
2049:
2048:
2025:
2021:
2019:
2016:
2015:
1999:
1996:
1995:
1984:
1970:
1937:
1933:
1931:
1928:
1927:
1908:
1904:
1902:
1899:
1898:
1880:
1877:
1876:
1847:
1844:
1843:
1823:
1820:
1819:
1801:
1798:
1797:
1761:
1758:
1757:
1732:
1730:
1729:
1721:
1719:
1716:
1715:
1699:
1696:
1695:
1679:
1677:
1674:
1673:
1651:
1649:
1648:
1646:
1643:
1642:
1626:
1623:
1622:
1552:
1548:
1537:
1535:
1532:
1531:
1514:
1511:
1510:
1482:
1479:
1478:
1462:
1459:
1458:
1455:
1435:Brownian motion
1422:
1396:
1340:
1337:
1336:
1307:
1304:
1303:
1286:
1283:
1282:
1266:
1263:
1262:
1253:
1219:
1208:
1205:
1204:
1182:
1171:
1168:
1167:
1135:
1124:
1121:
1120:
1104:
1101:
1100:
1089:
1076:
1075:
1052:
1026:
1008:
1007:
993:
983:
971:
945:
935:
933:
926:
909:
896:
894:
891:
890:
879:, to yield the
870:
840:
814:
810:
808:
805:
804:
788:
785:
784:
756:
752:
750:
747:
746:
725:
721:
719:
716:
715:
702:rooted at node
696:
674:
670:
658:
654:
645:
641:
636:
630:
626:
606:
602:
601:
591:
587:
575:
571:
562:
558:
553:
547:
543:
523:
519:
518:
513:
509:
500:
496:
476:
472:
471:
458:
454:
452:
449:
448:
405:
316:
286:
280:
215:
162:of proteins by
148:
22:(also known as
17:
12:
11:
5:
9658:
9648:
9647:
9642:
9637:
9632:
9627:
9612:
9611:
9539:
9486:van 't Wout AB
9476:
9441:(2): 114โ124.
9425:
9356:
9305:
9256:
9235:(1): 130โ131.
9229:Bioinformatics
9215:
9164:
9113:
9086:Bioinformatics
9072:
9045:(2): 214โ223.
9029:
9002:Bioinformatics
8988:
8951:(6): 617โ628.
8935:
8900:(2): 848โ850.
8884:
8833:
8782:
8733:
8682:
8667:
8616:
8567:
8540:Bioinformatics
8526:
8474:
8459:
8438:(5): 676โ679.
8432:Bioinformatics
8418:
8389:
8344:
8326:
8287:(7): 448โ450.
8264:
8233:(4): 544โ561.
8208:
8159:
8141:
8110:(2): 131โ158.
8090:
8069:(5): 693โ707.
8044:
7987:
7938:
7887:
7858:(3): 306โ310.
7838:
7819:(6): 657โ666.
7803:
7796:
7768:
7749:(3): 311โ313.
7733:
7692:
7643:
7590:
7569:(2): 438โ449.
7549:
7500:
7449:
7408:
7359:
7318:
7259:
7208:
7149:
7105:
7046:
7027:(3): 349โ358.
7011:
6984:(4): 309โ317.
6968:
6941:(3): 539โ557.
6925:
6910:
6875:
6864:(3): 304โ314.
6848:
6805:
6790:
6761:
6710:
6667:
6640:(6): 493โ503.
6623:
6557:
6548:
6537:(3): 265โ292.
6521:
6494:
6481:10.1086/285670
6475:(2): 193โ209.
6456:
6425:(5): 701โ710.
6405:
6356:
6307:
6282:Acta Zoologica
6272:
6253:(2): 301โ313.
6237:
6210:(2): 397โ405.
6194:
6151:
6102:
6051:
6022:(3): 351โ366.
6003:
5982:(5): 555โ556.
5962:
5941:(8): 754โ755.
5935:Bioinformatics
5921:
5870:
5845:Bioinformatics
5834:
5799:(6): 686โ690.
5783:
5748:(6): 368โ376.
5729:
5710:(3): 333โ348.
5690:
5659:(5): 696โ704.
5639:
5618:(3): 612โ622.
5595:
5550:(2): 313โ320.
5534:
5478:
5457:10.1086/284325
5432:
5395:(4): 647โ653.
5379:
5357:10.1.1.594.175
5350:(3): 623โ633.
5334:
5299:(9): 361โ366.
5278:
5251:(3): 240โ249.
5235:
5183:
5138:
5111:Bioinformatics
5094:
5067:(4): 406โ416.
5048:
5029:(2): 199โ229.
5013:
4983:10.1.1.22.6143
4976:(3): 581โ607.
4960:
4914:
4852:
4796:
4777:(9): 475โ481.
4761:
4695:
4666:(3): 360โ366.
4646:
4594:
4553:
4524:(3): 509โ518.
4504:
4473:(5): 673โ684.
4448:
4429:(6): 890โ896.
4408:
4373:(2): 135โ136.
4357:
4298:
4259:(11): e78871.
4239:
4212:(4): 380โ385.
4196:
4145:
4124:(3): 604โ611.
4100:
4013:
4010:
4009:
4008:
4003:
3998:
3996:Origin of life
3993:
3987:
3986:
3970:
3967:
3951:
3948:
3934:
3931:
3902:phylogeography
3878:
3875:
3853:
3850:
3848:
3845:
3842:
3841:
3838:
3835:
3832:
3827:
3824:
3821:
3815:
3814:
3811:
3808:
3805:
3804:FASTA, GenBank
3802:
3801:Unix, Mac, Win
3799:
3796:
3790:
3789:
3786:
3783:
3780:
3775:
3772:
3769:
3763:
3762:
3759:
3756:
3753:
3750:
3747:
3744:
3738:
3737:
3734:
3731:
3728:
3725:
3724:Unix, Mac, Win
3722:
3719:
3713:
3712:
3709:
3706:
3703:
3698:
3697:Unix, Mac, Win
3695:
3692:
3686:
3685:
3682:
3679:
3676:
3671:
3668:
3665:
3659:
3658:
3655:
3652:
3649:
3646:
3643:
3640:
3634:
3633:
3630:
3627:
3624:
3621:
3618:
3615:
3609:
3608:
3605:
3602:
3599:
3596:
3595:Unix, Mac, Win
3593:
3590:
3584:
3583:
3578:
3575:
3572:
3569:
3568:Unix, Mac, Win
3566:
3563:
3556:
3555:
3553:Apache License
3550:
3547:
3544:
3541:
3540:Unix, Mac, Win
3538:
3535:
3529:
3528:
3525:
3522:
3519:
3516:
3515:Unix, Mac, Win
3513:
3510:
3504:
3503:
3500:
3497:
3494:
3489:
3486:
3483:
3477:
3476:
3473:
3470:
3467:
3464:
3461:
3458:
3452:
3451:
3448:
3445:
3442:
3439:
3436:
3433:
3427:
3426:
3423:
3420:
3417:
3414:
3413:Unix, Mac, Win
3411:
3408:
3402:
3401:
3398:
3395:
3389:
3386:
3385:Unix, Mac, Win
3383:
3380:
3374:
3373:
3370:
3367:
3364:
3361:
3358:
3355:
3349:
3348:
3343:
3340:
3337:
3334:
3333:Unix, Mac, Win
3331:
3328:
3322:
3321:
3315:
3312:
3309:
3306:
3305:Unix, Mac, Win
3303:
3300:
3294:
3293:
3290:
3287:
3284:
3281:
3280:Unix, Mac, Win
3278:
3275:
3269:
3268:
3263:
3260:
3257:
3254:
3253:Unix, Mac, Win
3251:
3248:
3242:
3241:
3236:
3233:
3230:
3229:newick, nexus
3227:
3224:
3221:
3215:
3214:
3209:
3206:
3203:
3200:
3199:Unix, Mac, Win
3197:
3194:
3188:
3187:
3181:
3178:
3175:
3172:
3171:Unix, Mac, Win
3169:
3166:
3160:
3159:
3154:
3151:
3148:
3145:
3142:
3139:
3124:
3121:
3091:
3088:
3028:
3027:Species ranges
3025:
2992:
2989:
2987:
2984:
2930:
2927:
2904:
2903:Vaccine design
2901:
2863:
2860:
2847:
2844:
2822:
2819:
2815:horned lizards
2795:
2792:
2751:
2748:
2729:
2726:
2699:
2696:
2694:
2691:
2690:
2689:
2682:stable process
2674:
2662:
2642:
2622:
2602:
2582:
2560:
2556:
2535:
2515:
2495:
2475:
2455:
2437:
2423:
2419:
2398:
2393:
2389:
2368:
2348:
2328:
2308:
2288:
2268:
2248:
2228:
2208:
2188:
2160:
2157:
2154:
2151:
2131:
2128:
2123:
2119:
2098:
2095:
2092:
2089:
2069:
2066:
2061:
2057:
2036:
2033:
2028:
2024:
2003:
1983:
1980:
1969:
1966:
1965:
1964:
1936:
1907:
1884:
1872:
1851:
1827:
1805:
1780:
1777:
1774:
1771:
1768:
1765:
1739:
1735:
1728:
1724:
1703:
1682:
1658:
1654:
1630:
1599:
1596:
1593:
1590:
1587:
1584:
1581:
1578:
1575:
1572:
1569:
1566:
1563:
1558:
1555:
1551:
1547:
1544:
1540:
1518:
1498:
1495:
1492:
1489:
1486:
1466:
1454:
1451:
1421:
1418:
1395:
1392:
1344:
1320:
1317:
1314:
1311:
1290:
1270:
1252:
1249:
1229:
1226:
1222:
1218:
1215:
1212:
1192:
1189:
1185:
1181:
1178:
1175:
1151:
1148:
1145:
1142:
1138:
1134:
1131:
1128:
1108:
1074:
1071:
1068:
1065:
1062:
1059:
1055:
1051:
1048:
1045:
1042:
1039:
1036:
1033:
1029:
1025:
1022:
1019:
1016:
1013:
1011:
1009:
1003:
1000:
996:
992:
989:
986:
981:
978:
974:
970:
967:
964:
961:
958:
955:
952:
948:
944:
941:
938:
932:
929:
927:
925:
922:
919:
916:
912:
908:
905:
902:
899:
898:
889:
885:Bayes' theorem
869:
866:
839:
836:
817:
813:
792:
762:
759:
755:
728:
724:
683:
677:
673:
669:
664:
661:
657:
653:
648:
644:
639:
633:
629:
625:
622:
617:
614:
609:
605:
600:
594:
590:
586:
581:
578:
574:
570:
565:
561:
556:
550:
546:
542:
539:
534:
531:
526:
522:
517:
512:
508:
503:
499:
495:
492:
487:
484:
479:
475:
470:
466:
461:
457:
446:
430:Markov process
404:
401:
400:
399:
392:
386:
379:
369:
314:
301:Fitch's method
282:Main article:
279:
276:
243:internal nodes
235:terminal nodes
214:
211:
207:phylogeography
147:
144:
15:
9:
6:
4:
3:
2:
9657:
9646:
9643:
9641:
9638:
9636:
9633:
9631:
9628:
9626:
9623:
9622:
9620:
9607:
9603:
9598:
9593:
9588:
9583:
9579:
9575:
9570:
9565:
9561:
9557:
9553:
9549:
9543:
9535:
9531:
9526:
9521:
9516:
9511:
9507:
9503:
9499:
9495:
9491:
9487:
9480:
9472:
9468:
9464:
9460:
9456:
9452:
9448:
9444:
9440:
9436:
9429:
9421:
9417:
9412:
9407:
9402:
9397:
9393:
9389:
9384:
9379:
9375:
9371:
9367:
9360:
9352:
9348:
9343:
9338:
9333:
9328:
9324:
9320:
9316:
9309:
9301:
9297:
9292:
9287:
9283:
9279:
9275:
9271:
9267:
9260:
9252:
9248:
9243:
9238:
9234:
9230:
9226:
9219:
9211:
9207:
9202:
9197:
9192:
9187:
9183:
9179:
9175:
9168:
9160:
9156:
9151:
9146:
9141:
9136:
9132:
9128:
9124:
9117:
9109:
9105:
9100:
9095:
9091:
9087:
9083:
9076:
9068:
9064:
9060:
9056:
9052:
9048:
9044:
9040:
9033:
9025:
9021:
9016:
9011:
9007:
9003:
8999:
8992:
8984:
8980:
8976:
8972:
8967:
8962:
8958:
8954:
8950:
8946:
8939:
8931:
8927:
8923:
8919:
8915:
8911:
8907:
8903:
8899:
8895:
8888:
8880:
8876:
8872:
8868:
8864:
8860:
8856:
8852:
8848:
8844:
8837:
8829:
8825:
8821:
8817:
8813:
8809:
8805:
8801:
8797:
8793:
8786:
8778:
8774:
8769:
8764:
8760:
8756:
8752:
8748:
8744:
8737:
8729:
8725:
8720:
8715:
8710:
8705:
8701:
8697:
8693:
8686:
8678:
8671:
8663:
8659:
8654:
8649:
8644:
8639:
8635:
8631:
8627:
8620:
8612:
8608:
8603:
8598:
8594:
8590:
8586:
8582:
8578:
8571:
8563:
8559:
8554:
8549:
8545:
8541:
8537:
8530:
8522:
8518:
8513:
8508:
8504:
8500:
8496:
8492:
8488:
8481:
8479:
8470:
8463:
8455:
8451:
8446:
8441:
8437:
8433:
8429:
8422:
8408:on 2015-03-07
8407:
8403:
8399:
8393:
8385:
8381:
8377:
8373:
8368:
8363:
8359:
8355:
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8318:
8313:
8308:
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8298:
8294:
8290:
8286:
8282:
8278:
8271:
8269:
8260:
8256:
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8241:
8236:
8232:
8228:
8224:
8217:
8215:
8213:
8204:
8200:
8196:
8192:
8187:
8182:
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8133:
8128:
8123:
8118:
8113:
8109:
8105:
8101:
8094:
8086:
8082:
8077:
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8068:
8064:
8060:
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8051:
8049:
8040:
8036:
8031:
8026:
8022:
8018:
8014:
8010:
8006:
8002:
7998:
7991:
7983:
7979:
7974:
7969:
7965:
7961:
7957:
7953:
7949:
7942:
7934:
7930:
7926:
7922:
7918:
7914:
7910:
7906:
7902:
7898:
7891:
7883:
7879:
7874:
7869:
7865:
7861:
7857:
7853:
7849:
7842:
7834:
7830:
7826:
7822:
7818:
7814:
7807:
7799:
7797:9780262258753
7793:
7789:
7785:
7782:. MIT Press.
7781:
7780:
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6791:9780121828004
6787:
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5070:
5066:
5062:
5055:
5053:
5044:
5040:
5036:
5032:
5028:
5024:
5017:
5009:
5005:
5001:
4997:
4993:
4989:
4984:
4979:
4975:
4971:
4964:
4956:
4952:
4948:
4944:
4940:
4936:
4932:
4928:
4921:
4919:
4910:
4906:
4901:
4896:
4891:
4886:
4882:
4878:
4874:
4870:
4866:
4859:
4857:
4848:
4844:
4839:
4834:
4829:
4824:
4820:
4816:
4812:
4805:
4803:
4801:
4792:
4788:
4784:
4780:
4776:
4772:
4765:
4757:
4753:
4748:
4743:
4738:
4733:
4729:
4725:
4721:
4717:
4713:
4706:
4704:
4702:
4700:
4691:
4687:
4682:
4677:
4673:
4669:
4665:
4661:
4657:
4650:
4642:
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4633:
4628:
4624:
4620:
4616:
4612:
4608:
4601:
4599:
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4586:
4581:
4576:
4572:
4568:
4564:
4557:
4549:
4545:
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4523:
4519:
4515:
4508:
4500:
4496:
4491:
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4476:
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4468:
4464:
4457:
4455:
4453:
4444:
4440:
4436:
4432:
4428:
4424:
4417:
4415:
4413:
4404:
4400:
4396:
4392:
4388:
4384:
4380:
4376:
4372:
4368:
4361:
4353:
4349:
4344:
4339:
4334:
4329:
4325:
4321:
4318:(4): e19066.
4317:
4313:
4309:
4302:
4294:
4290:
4285:
4280:
4275:
4270:
4266:
4262:
4258:
4254:
4250:
4243:
4235:
4231:
4227:
4223:
4219:
4215:
4211:
4207:
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4192:
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4183:
4178:
4173:
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4160:
4156:
4149:
4141:
4137:
4132:
4127:
4123:
4119:
4115:
4108:
4106:
4101:
4099:
4095:
4091:
4087:
4083:
4078:
4073:
4069:
4065:
4060:
4055:
4051:
4047:
4046:
4041:
4035:
4031:
4026:
4019:
4007:
4004:
4002:
3999:
3997:
3994:
3992:
3989:
3988:
3984:
3978:
3973:
3966:
3963:
3958:
3947:
3945:
3941:
3930:
3927:
3922:
3919:
3915:
3911:
3907:
3903:
3898:
3896:
3892:
3888:
3884:
3874:
3870:
3868:
3864:
3860:
3839:
3836:
3833:
3831:
3828:
3825:
3822:
3820:
3817:
3816:
3812:
3809:
3806:
3803:
3800:
3797:
3795:
3792:
3791:
3787:
3784:
3781:
3779:
3776:
3773:
3770:
3768:
3765:
3764:
3760:
3757:
3754:
3751:
3748:
3745:
3743:
3740:
3739:
3735:
3732:
3729:
3726:
3723:
3720:
3718:
3715:
3714:
3710:
3707:
3704:
3702:
3699:
3696:
3693:
3691:
3688:
3687:
3683:
3680:
3677:
3675:
3672:
3669:
3666:
3664:
3661:
3660:
3656:
3653:
3650:
3647:
3644:
3641:
3639:
3636:
3635:
3631:
3628:
3625:
3622:
3619:
3616:
3614:
3611:
3610:
3606:
3603:
3600:
3597:
3594:
3591:
3589:
3586:
3585:
3582:
3579:
3576:
3573:
3570:
3567:
3564:
3561:
3558:
3557:
3554:
3551:
3548:
3545:
3542:
3539:
3536:
3534:
3531:
3530:
3526:
3523:
3520:
3517:
3514:
3511:
3509:
3506:
3505:
3501:
3498:
3495:
3493:
3490:
3487:
3484:
3482:
3479:
3478:
3474:
3471:
3468:
3465:
3462:
3459:
3457:
3454:
3453:
3449:
3446:
3443:
3440:
3437:
3434:
3432:
3429:
3428:
3424:
3421:
3418:
3415:
3412:
3409:
3407:
3404:
3403:
3399:
3396:
3394:
3390:
3387:
3384:
3381:
3379:
3376:
3375:
3371:
3368:
3365:
3362:
3359:
3356:
3354:
3351:
3350:
3347:
3344:
3341:
3338:
3335:
3332:
3329:
3327:
3324:
3323:
3319:
3316:
3313:
3310:
3307:
3304:
3301:
3299:
3296:
3295:
3291:
3288:
3285:
3282:
3279:
3276:
3274:
3271:
3270:
3267:
3264:
3261:
3258:
3255:
3252:
3249:
3247:
3244:
3243:
3240:
3237:
3234:
3231:
3228:
3225:
3222:
3220:
3217:
3216:
3213:
3210:
3207:
3204:
3201:
3198:
3195:
3193:
3190:
3189:
3185:
3182:
3179:
3176:
3173:
3170:
3167:
3165:
3162:
3161:
3158:
3155:
3152:
3149:
3146:
3143:
3140:
3137:
3136:
3133:
3131:
3120:
3118:
3114:
3110:
3106:
3101:
3097:
3087:
3084:
3075:
3071:
3066:
3062:
3060:
3059:
3052:
3050:
3045:
3040:
3039:
3034:
3033:biogeographic
3024:
3022:
3018:
3014:
3009:
3005:
3003:
2999:
2983:
2981:
2977:
2972:
2967:
2965:
2961:
2957:
2953:
2952:recombination
2949:
2948:transposition
2945:
2941:
2937:
2926:
2923:
2918:
2914:
2910:
2900:
2897:
2893:
2888:
2884:
2882:
2878:
2874:
2869:
2859:
2856:
2852:
2843:
2841:
2836:
2832:
2828:
2818:
2816:
2812:
2808:
2804:
2800:
2799:Phrynosomatid
2791:
2789:
2788:
2783:
2782:
2777:
2773:
2769:
2765:
2761:
2757:
2747:
2745:
2741:
2740:
2735:
2725:
2723:
2719:
2715:
2710:
2709:
2704:
2687:
2683:
2678:
2675:
2660:
2640:
2620:
2600:
2580:
2558:
2554:
2533:
2513:
2493:
2473:
2453:
2445:
2441:
2438:
2421:
2417:
2396:
2391:
2387:
2379:and variance
2366:
2346:
2326:
2306:
2286:
2266:
2246:
2226:
2206:
2186:
2178:
2175:
2174:
2158:
2155:
2152:
2149:
2129:
2126:
2121:
2117:
2096:
2093:
2090:
2087:
2067:
2064:
2059:
2055:
2034:
2031:
2026:
2022:
2001:
1992:
1988:
1979:
1976:
1959:
1934:
1905:
1896:
1882:
1873:
1866:
1849:
1841:
1825:
1817:
1803:
1794:
1793:
1792:
1775:
1772:
1769:
1763:
1754:
1726:
1701:
1628:
1615:
1611:
1594:
1591:
1588:
1585:
1582:
1579:
1576:
1573:
1570:
1567:
1564:
1561:
1556:
1553:
1549:
1542:
1516:
1496:
1493:
1490:
1487:
1484:
1464:
1450:
1448:
1444:
1440:
1436:
1432:
1428:
1417:
1415:
1409:
1407:
1402:
1391:
1389:
1388:chain samples
1385:
1379:
1375:
1373:
1369:
1368:lichenization
1365:
1360:
1356:
1342:
1334:
1315:
1309:
1288:
1268:
1259:
1248:
1245:
1241:
1224:
1216:
1210:
1187:
1179:
1173:
1165:
1146:
1143:
1140:
1132:
1126:
1106:
1098:
1094:
1069:
1063:
1057:
1049:
1043:
1037:
1034:
1031:
1023:
1017:
1014:
1012:
998:
990:
984:
976:
968:
962:
956:
953:
950:
942:
936:
930:
928:
920:
917:
914:
906:
900:
888:
886:
882:
878:
874:
865:
861:
859:
853:
850:
846:
835:
833:
815:
811:
782:
778:
760:
757:
753:
744:
726:
722:
713:
709:
705:
701:
695:
681:
675:
671:
662:
659:
655:
651:
646:
642:
631:
627:
620:
612:
607:
603:
598:
592:
588:
579:
576:
572:
568:
563:
559:
548:
544:
537:
529:
524:
520:
515:
510:
501:
497:
490:
482:
477:
473:
468:
464:
459:
455:
445:
443:
439:
435:
431:
426:
424:
420:
415:
413:
409:
396:
393:
390:
387:
383:
380:
377:
373:
370:
367:
366:transversions
363:
358:
355:
354:
353:
349:
340:
336:
333:
329:
325:
321:
317:
310:
306:
302:
297:
295:
291:
290:Occam's razor
285:
275:
273:
269:
265:
260:
257:
251:
248:
244:
240:
236:
232:
228:
224:
220:
210:
208:
204:
200:
194:
192:
191:
186:
182:
178:
174:
169:
165:
161:
157:
156:Linus Pauling
153:
143:
141:
136:
132:
128:
124:
120:
115:
111:
110:phylogenetics
107:
104:
99:
97:
92:
89:
85:
81:
77:
73:
69:
65:
61:
57:
53:
49:
45:
41:
40:phylogenetics
37:
33:
32:
27:
26:
21:
9559:
9555:
9542:
9497:
9493:
9479:
9438:
9434:
9428:
9373:
9369:
9359:
9322:
9318:
9308:
9273:
9269:
9259:
9232:
9228:
9218:
9181:
9177:
9167:
9130:
9126:
9116:
9089:
9085:
9075:
9042:
9038:
9032:
9005:
9001:
8991:
8948:
8944:
8938:
8897:
8893:
8887:
8846:
8842:
8836:
8795:
8791:
8785:
8750:
8746:
8736:
8699:
8695:
8685:
8676:
8670:
8633:
8629:
8619:
8587:(1): 41โ51.
8584:
8580:
8570:
8543:
8539:
8529:
8494:
8490:
8462:
8435:
8431:
8421:
8410:. Retrieved
8406:the original
8401:
8392:
8357:
8353:
8347:
8338:
8284:
8280:
8230:
8226:
8176:
8172:
8162:
8154:
8144:
8107:
8103:
8093:
8066:
8062:
8004:
8000:
7990:
7955:
7951:
7941:
7900:
7896:
7890:
7855:
7851:
7841:
7816:
7812:
7806:
7778:
7771:
7746:
7742:
7736:
7712:(1): 26โ36.
7709:
7705:
7695:
7660:
7656:
7646:
7611:
7607:
7593:
7566:
7562:
7552:
7517:
7513:
7503:
7462:
7458:
7452:
7425:
7421:
7411:
7376:
7372:
7362:
7335:
7331:
7321:
7276:
7272:
7262:
7221:
7217:
7211:
7169:(11): e231.
7166:
7162:
7152:
7125:
7121:
7108:
7063:
7059:
7049:
7024:
7020:
7014:
6981:
6977:
6971:
6938:
6934:
6928:
6919:
6913:
6888:
6884:
6878:
6861:
6857:
6851:
6818:
6814:
6808:
6773:
6727:
6723:
6713:
6683:(1): 37โ45.
6680:
6676:
6670:
6637:
6633:
6626:
6581:
6577:
6551:
6534:
6530:
6524:
6507:
6503:
6497:
6472:
6468:
6422:
6418:
6408:
6373:
6369:
6359:
6324:
6320:
6310:
6285:
6281:
6275:
6250:
6246:
6240:
6207:
6203:
6197:
6164:
6160:
6154:
6119:
6115:
6105:
6064:
6060:
6054:
6019:
6015:
5979:
5975:
5965:
5938:
5934:
5924:
5887:
5883:
5873:
5848:
5844:
5837:
5796:
5792:
5786:
5745:
5741:
5707:
5703:
5693:
5656:
5652:
5642:
5615:
5611:
5547:
5543:
5537:
5502:
5498:
5448:
5444:
5392:
5388:
5382:
5347:
5343:
5337:
5296:
5292:
5248:
5244:
5238:
5205:
5201:
5154:(1): 35โ42.
5151:
5147:
5141:
5114:
5110:
5097:
5064:
5060:
5026:
5022:
5016:
4973:
4969:
4963:
4930:
4926:
4872:
4868:
4818:
4814:
4774:
4770:
4764:
4719:
4715:
4663:
4659:
4649:
4617:(1): 28โ64.
4614:
4610:
4570:
4566:
4556:
4521:
4517:
4507:
4470:
4466:
4426:
4422:
4370:
4366:
4360:
4315:
4311:
4301:
4256:
4252:
4242:
4209:
4205:
4199:
4162:
4158:
4148:
4121:
4117:
4049:
4043:
4015:
3953:
3936:
3923:
3899:
3894:
3886:
3880:
3871:
3858:
3855:
3761:Proprietary
3502:Proprietary
3475:Proprietary
3186:, version 3
3126:
3093:
3079:
3057:
3053:
3048:
3036:
3030:
3010:
3006:
3002:rabies virus
2994:
2979:
2968:
2936:permutations
2932:
2921:
2906:
2889:
2885:
2865:
2849:
2835:stable model
2824:
2797:
2785:
2781:Camarhynchus
2779:
2772:insectivores
2753:
2737:
2731:
2721:
2717:
2711:
2707:
2702:
2701:
2693:Applications
2676:
2443:
2439:
2176:
1985:
1971:
1874:
1840:Jukes-Cantor
1795:
1755:
1620:
1456:
1427:Markov chain
1423:
1410:
1397:
1380:
1376:
1357:
1332:
1254:
1246:
1242:
1096:
1092:
1090:
871:
862:
854:
844:
841:
831:
780:
776:
742:
711:
707:
703:
697:
447:
441:
437:
433:
427:
423:transversion
416:
406:
394:
388:
381:
375:
371:
356:
350:
346:
319:
312:
298:
287:
261:
252:
242:
238:
234:
230:
216:
195:
188:
149:
100:
93:
44:evolutionary
30:
29:
24:
23:
19:
18:
8966:11336/70196
6510:: 445โ471.
6288:: 357โ384.
5451:(1): 1โ15.
4821:(1): 4โ14.
3782:Genome maps
3581:BSD License
3406:Phylomapper
3326:BayesTraits
3273:Diversitree
3109:orthologous
3021:West Africa
2956:duplication
2881:co-evolving
2855:Felsenstein
2444:stabilizing
1445:methods or
1406:plaque size
1394:Calibration
858:heterotachy
362:transitions
305:binary tree
103:statistical
78:), and the
9619:Categories
9548:Schwarz RF
9325:(1): 354.
9133:: 167408.
8945:Cladistics
8702:(1): 127.
8412:2019-03-07
6584:(1): 226.
5907:10092/2637
4933:(1): 1โ7.
4722:(6): e69.
4012:References
3883:phenotypes
3807:Nucleotide
3657:Copyright
3626:Geographic
3620:Linux, Win
3601:Geographic
3574:Nucleotide
3393:Geographic
3366:Geographic
3074:Dobzhansky
3070:Sturtevant
2980:Candidatus
2890:Ancestral
2803:fiber type
2768:granivores
2744:viviparity
2739:Phrynosoma
2732:In horned
1431:brain size
1302:computing
745:-th node,
419:transition
223:hypothesis
173:cladistics
9569:1306.1685
9383:1207.6327
9184:(1): 25.
8871:0962-8452
8820:2041-210X
8636:(1): 88.
8362:CiteSeerX
8235:CiteSeerX
8112:CiteSeerX
7763:0196-6774
6427:CiteSeerX
6302:0001-7272
6232:198153271
6024:CiteSeerX
5724:0167-9473
5661:CiteSeerX
5634:1063-5157
5560:CiteSeerX
5465:0003-0147
5402:0803.0195
5374:1063-5157
5352:CiteSeerX
5265:0039-7989
5178:0036-1399
5156:CiteSeerX
5081:0039-7989
5043:0025-5564
5008:189885872
4978:CiteSeerX
4955:0022-5193
4823:CiteSeerX
4589:0904-213X
4475:CiteSeerX
4387:0376-6357
4226:0039-7989
4165:(1): 33.
4140:1063-5157
4094:Q28596371
4068:1553-734X
4028:license (
4025:CC BY 4.0
3645:Web, Unix
3562:(PREQUEL)
3431:Ancestors
3083:fruit fly
3049:Cyrtandra
3038:Cyrtandra
3017:Hong Kong
3013:Guangdong
2991:Migration
2971:karyotype
2940:inversion
2922:ancestral
2776:folivores
2633:tends to
2621:α
2581:α
2555:σ
2418:σ
2388:σ
2171:(orange).
2156:−
2150:α
2118:σ
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