Phylogeny. Discrete and random processes in evolution
The author describes some of the key problems in phylogenetics. He defines this scientific area as ``the theory of reconstructing and analyzing trees or more complex networks from data observed in the present.NEWLINENEWLINEIn Chapter 1, basic concepts are presented: generic and key notation, graphs and trees, phylogenetic trees.NEWLINENEWLINEChapter 2 describes some combinatorial features of phylogenetic trees, encoding by set systems, enumeration, properties of tree shape, and metrics on trees. Counting trees, rooted and unrooted trees, tree rearrangement metrics, and consensus functions are studied.NEWLINENEWLINEIn Chapter 3, the author discusses discrete properties of phylogenetic trees that arise under random models of evolution. Particularly, he describes tree shapes, including evolving trees, measuring, and modelling tree shape.NEWLINENEWLINEIn Chapter 4, results of exploration trees in terms of their substructures are given.NEWLINENEWLINEChapter 5 studies the way in which trees can display discrete data and focuses on tree reconstruction from data, which may not perfectly fit tree characters, homoplasy, and minimal evolution trees, including trees for a sequence of characters.NEWLINENEWLINEChapter 6 ``allows edges of a tree to have length, a seemingly minor embellishment which leads to enhanced theory for tree reconstruction, geometric modeling, and biodiversity conversation. The author defines metrics from trees with edge lengths, and describes three distance-based tree reconstruction methods. At the end of the chapter, a generalization and geometry approaches are presented; this part of the book ends with a description of phylogenetic diversity.NEWLINENEWLINEIn Chapter 7, the author discusses stochastic models which can describe the evolution of discrete characters as they evolve along the branches of evolutionary trees from some unknown ancestral state. Using such models, simple empirical distances can be transformed in such a way that methods like NJ applied to these transformed distances are statistically consistent estimators of phylogenies and branch length. He describes nonhomogeneous Markov chains, Hadamard story and phylogenetic mixture models.NEWLINENEWLINEIn Chapter 8, the author continues the application of Markov processes to trees, focusing on the points of view of information theory and algebra. In these two chapters about Markov processes on trees, many topics have been omitted, including bootstrap, model selection, the theory underlying the VCVC machinery in Bayesian phylogenetics, and the evolution of continuous characters based on stochastic models.NEWLINENEWLINEChapter 9 presents results ``of speciation and extinction models for phylogenies, and the predictions these make regarding the trees' shape. Also was investigated random processes under which gene and species trees can disagree.NEWLINENEWLINEIn Chapter 10, the author considers a framework allowing more complex representations of evolutionary relationships. The author indicates that a directed network can provide an explicit representation of evolution where there has been reticulation. In this part, the main concepts and results as well as a number of recent developments are described.
- Enumeration of lonely pairs of gene trees and species trees by means of antipodal cherries
- Treewidth distance on phylogenetic trees
- Solving the tree containment problem in linear time for nearly stable phylogenetic networks
- Necessary and sufficient conditions for consistent root reconstruction in Markov models on trees
- Probabilistic models for the (sub)tree(s) of life
- Comparing the rankings obtained from two biodiversity indices: the fair proportion index and the Shapley value
- Lie-Markov models derived from finite semigroups
- Mathematical and simulation-based analysis of the behavior of admixed taxa in the neighbor-joining algorithm
- Identifying species network features from gene tree quartets under the coalescent model
- On the Shapley value of unrooted phylogenetic trees
- Species notions that combine phylogenetic trees and phenotypic partitions
- Deciding the existence of a cherry-picking sequence is hard on two trees
- Quantifying the accuracy of ancestral state prediction in a phylogenetic tree under maximum parsimony
- Bounds for phylogenetic network space metrics
- The matroid structure of representative triple sets and triple-closure computation
- Inferring phylogenetic trees from the knowledge of rare evolutionary events
- Evolutionary isolation and phylogenetic diversity loss under random extinction events
- Reconstructing gene trees from Fitch's xenology relation
- On cherry and pitchfork distributions of random rooted and unrooted phylogenetic trees
- Character-based phylogeny construction and its application to tumor evolution
- Extremal values of the Sackin tree balance index
- Galois connections for phylogenetic networks and their polytopes
- Sufficient condition for root reconstruction by parsimony on binary trees with general weights
- Measuring tree balance using symmetry nodes -- a new balance index and its extremal properties
- A simple derivation of the mean of the Sackin index of tree balance under the uniform model on rooted binary labeled trees
- Merging arcs to produce acyclic phylogenetic networks and normal networks
- The edge-product space of phylogenetic trees is not shellable
- Distinct-cluster tree-child phylogenetic networks and possible uses to study polyploidy
- Encoding and ordering X-cactuses
- Identifiability of local and global features of phylogenetic networks from average distances
- Two results about the Sackin and Colless indices for phylogenetic trees and their shapes
- The tree of blobs of a species network: identifiability under the coalescent
- The distributions under two species-tree models of the number of root ancestral configurations for matching gene trees and species trees
- Species tree estimation under joint modeling of coalescence and duplication: sample complexity of quartet methods
- An impossibility result for phylogeny reconstruction from \(k\)-mer counts
- Information metrics for phylogenetic trees via distributions of discrete and continuous characters
- Sharp upper and lower bounds on a restricted class of convex characters
- Identifiability of species network topologies from genomic sequences using the logDet distance
- A stochastic Farris transform for genetic data under the multispecies coalescent with applications to data requirements
- Classes of explicit phylogenetic networks and their biological and mathematical significance
- Enumeration of binary trees compatible with a perfect phylogeny
- Bijections for ranked tree-child networks
- Counting and optimising maximum phylogenetic diversity sets
- The Sackin index of simplex networks
- An algorithm for reconstructing level-2 phylogenetic networks from trinets
- On the effect of intralocus recombination on triplet-based species tree estimation
- From modular decomposition trees to level-1 networks: pseudo-cographs, polar-cats and prime polar-cats
- Combinatorial views on persistent characters in phylogenetics
- On the minimum value of the Colless index and the bifurcating trees that achieve it
- \( F_{S T}\) and the triangle inequality for biallelic markers
- Phylogenetics of artificial manuscripts
- The space of tree-based phylogenetic networks
- How tree-based is my network? Proximity measures for unrooted phylogenetic networks
- Counting and enumerating galled networks
- Sequential importance sampling for multiresolution Kingman-Tajima coalescent counting
- Counting and enumerating tree-child networks and their subclasses
- Impossibility of consistent distance estimation from sequence lengths under the TKF91 model
- Maximum parsimony distance on phylogenetic trees: a linear kernel and constant factor approximation algorithm
- Phylosymmetric algebras: mathematical properties of a new tool in phylogenetics
- Identifiability in phylogenetics using algebraic matroids
- Distinguishing level-1 phylogenetic networks on the basis of data generated by Markov processes
- On asymptotic joint distributions of cherries and pitchforks for random phylogenetic trees
- Roadblocked monotonic paths and the enumeration of coalescent histories for non-matching caterpillar gene trees and species trees
- Phylogenetic networks that are their own fold-ups
- Correlation between Shapley values of rooted phylogenetic trees under the beta-splitting model
- Combinatorial properties of phylogenetic diversity indices
- Embeddability and rate identifiability of Kimura 2-parameter matrices
- Level-1 phylogenetic networks and their balanced minimum evolution polytopes
- A partial order and cluster-similarity metric on rooted phylogenetic trees
- Notes on Markov embedding
- Distribution and asymptotic behavior of the phylogenetic transfer distance
- Alternative characterizations of Fitch's xenology relation
- Generalized Fitch graphs: edge-labeled graphs that are explained by edge-labeled trees
- Reconciling event-labeled gene trees with MUL-trees and species networks
- The optimal rate for resolving a near-polytomy in a phylogeny
- On the distribution of interspecies correlation for Markov models of character evolution on Yule trees
- A note on the relaxation time of two Markov chains on rooted phylogenetic tree spaces
- Accumulation phylogenies
- Rooted NNI moves and distance-1 tail moves on tree-based phylogenetic networks
- Squaring within the Colless index yields a better balance index
- On the Colijn-Plazzotta numbering scheme for unlabeled binary rooted trees
- The rigid hybrid number for two phylogenetic trees
- The hybrid number of a ploidy profile
- The shape of phylogenies under phase-type distributed times to speciation and extinction
- Forest-based networks
- Cyclic generators and an improved linear kernel for the rooted subtree prune and regraft distance
- Parsimony and the rank of a flattening matrix
- The embedding problem for Markov matrices
- Evaluation of the relative performance of the subflattenings method for phylogenetic inference
- Quantum field theory and phylogenetic branching
- How are we related?
- The agreement distance of unrooted phylogenetic networks
- Mathematics of evolution and phylogeny.
- Basic phylogenetic combinatorics.
- scientific article; zbMATH DE number 23012 (Why is no real title available?)
- scientific article; zbMATH DE number 1173732 (Why is no real title available?)
- Phylogenetic Inference, Selection Theory, and History of Science
- Multiplicatively closed Markov models must form Lie algebras
- scientific article; zbMATH DE number 2171552 (Why is no real title available?)
- scientific article; zbMATH DE number 1865935 (Why is no real title available?)
This page was built for publication: Phylogeny. Discrete and random processes in evolution
Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q2828468)
