Evolution and Molecular Phylogeny

The hypothesis that the rate of genetic change within a species is relatively constant over time.

The rate of molecular evolution can differ between different species.

The rate of molecular evolution can differ between different genes or proteins.

The molecular clock is only useful for comparing genes that have retained their function over time.

The study of evolutionary relationships between organisms or molecules using molecular biology techniques.

The branching pattern of a phylogenetic tree, showing the relationships between organisms or molecules.

A point on a phylogenetic tree where a new lineage diverges from a common ancestor.

A group of organisms or molecules descended from a common ancestor.

A graph representing evolutionary relationships between organisms, based on shared characteristics.

A branch connects two nodes and represents the evolutionary path between them. Its length indicates the amount of change.

A taxon (OTU) that is currently existing.

A taxon (OTU) that is extinct and only represented by an ancestral point.

The process of obtaining DNA or protein sequences from organisms to be used in phylogenetic analysis.

Aligning multiple sequences to identify similarities and differences, crucial for inferring evolutionary relationships.

Mathematical models used to estimate how DNA or protein sequences evolve over time, helping to create accurate phylogenetic trees.

Algorithms used to build phylogenetic trees based on the aligned sequences and evolutionary models.

Evaluating the reliability and accuracy of phylogenetic trees using statistical tests and visualization techniques.

Sequences used in phylogenetic analysis must share a common ancestor, meaning they are related by descent.

Distantly related sequences present challenges in MSA because aligning them accurately can be difficult. This is important when considering evolution over long periods.

Gaps in MSA can occur due to insertions or deletions in sequences, and must be carefully considered in phylogenetic analysis.

A measure of the genetic distance between two DNA sequences, representing the number of nucleotide differences.

A method that corrects for the underestimation of genetic distance caused by multiple mutations at a single site.

A model that estimates evolutionary distance by considering the probability of all possible nucleotide substitutions.

An extension of the Jukes-Cantor model that accounts for the different rates of transitions and transversions.

A model that adjusts for variations in the GC content of DNA sequences.

A model that acknowledges that different sites within a sequence can evolve at different rates.

Methods for constructing phylogenetic trees based on the genetic distances between sequences.

A method for building phylogenetic trees that does not assume a constant rate of evolution.

A statistical approach to modeling uncertainty in complex models. It incorporates prior information and uses computational methods to estimate the posterior probability distribution.

A method used in molecular phylogeny to estimate the reliability of branches in the tree. It generates multiple trees from random subsets of data and compares them to the original tree.

The tree with the highest likelihood of being correct based on the data.

A tree generated using Bayesian inference, reflecting the most probable evolutionary relationships based on the data and prior information.

A program for constructing phylogenetic trees that breaks down the problem into smaller groups (quartets) and then performs estimations of support for each group.

A sequence alignment, which serves as input for Bayesian methods, helps to define the prior model for the tree.

Generating the posterior probability distribution for a Bayesian method.

A method of constructing a phylogenetic tree that finds the tree with the shortest total branch lengths. This method assumes all taxa evolve at the same rate and all characters contribute equally to the information. It aims to minimize the number of evolutionary changes required to explain the observed data. This method is susceptible to long-branch attraction, where rapidly evolving taxa might be incorrectly grouped together.

A method of constructing a phylogenetic tree that aims to find the tree topology and branch lengths that have the highest probability of producing the observed data. It uses statistical models of evolutionary change that can vary across different parts of the tree. This method considers more complex evolutionary scenarios and is considered more accurate than parsimony methods.

A tree-building method that starts by calculating the pairwise distances between molecular sequences. The distances are then used to estimate branch lengths, with shorter distances indicating closer relationships.

A tree-building method that finds the tree with the shortest total branch lengths. This means it minimizes the number of evolutionary changes required to explain the observed data.

A tree-building method that aims to find the tree topology and branch lengths that have the highest probability of producing the observed data. It uses a statistical model of evolutionary change.

The Upweighted-Pair Group Method with Arithmetic Mean is a specific type of distance-based tree-building method. It is simple and fast but can be less accurate compared to other methods. It assumes a constant rate of evolution.

A method that does not assume a constant rate of evolution and is generally considered more accurate than UPGMA or other distance-based tree methods.