Evolution
Jack Kyte in Structure in Protein Chemistry, 2006
The amino acid sequences of a set of related polypeptides retain a record of the history of their evolution by natural selection. Evolution by natural selection is usually viewed from its optimistic side. The evolutionary distance between the amino acid sequences of two proteins is the value of any quantity that is thought to be directly proportional to the time that has elapsed since those proteins shared a common ancestor. If the nucleic acid sequence encoding either protein is unknown, mutations to an alternative codon for the same amino acid are also missed. The minimal mutational distances must be corrected statistically for all of these missing mutations to obtain estimates of evolutionary distances. The tabulated values of evolutionary distances are used to construct a tree the branches of which connect the species being compared. The phylogenetic tree, however, in addition to the historical sequence of events, conveys estimates of the evolutionary distances from existing species to common ancestors.
Importing Tree with Data
Guangchuang Yu in Data Integration, Manipulation and Visualization of Phylogenetic Trees, 2022
Phylogenetic trees are used to describe genealogical relationships among a group of organisms, which can be constructed based on the genetic sequences of the organisms. A rooted phylogenetic tree represents a model of evolutionary history depicted by ancestor-descendant relationships between tree nodes and clustering of sister' orcousin' organisms at a different level of relatedness. A phylogenetic tree can be constructed from genetic sequences using distance-based methods or character-based methods. The maximum likelihood method and Bayesian Markov Chain Monte Carlo method are the two most commonly used methods in phylogenetic tree construction and are most often used in scientific publications. Phylogenetic Analysis by Maximum Likelihood is a package of programs for phylogenetic analyses of DNA or protein sequences.
Phylogenetics
Dolly Sharma, Shailendra Singh, Mamta Mittal in Bioinformatics and RNA, 2021
This chapter elaborates on phylogenetics as a science of studying biological relationships between organisms. Further molecular phylogenetics is also explained. The chapter also focuses on phylogenetic tree construction. A step-by-step procedure for phylogenetic tree construction is explained using distance matrix methods and character-based methods. Molecular phylogenetics is a branch of phylogeny that analyzes the difference in molecular sequences, essentially in a DNA sequence to understand the evolutionary relationships. Over a period of time, molecular sequences observe mutations. In molecular phylogenetics, the rate of mutation in a molecular sequence is tracked in order to study evolutionary relationships among species. A mutation in a sequence refers to insertion, removal, inversion or replacement of nucleotides in a molecular sequence. Information is passed from generation to generation through gene evolution or through DNA sequence. Gene evolution results in paralogs, homologs and orthologs. Paralogs are homologous sequences that are related due to gene duplication.
Phylogenetic analyses: a brief introduction to methods and their application
Published in Expert Review of Molecular Diagnostics, 2004
David S Horner, Graziano Pesole
Phylogenetic analysis of molecular sequence data plays an increasingly important role in clinical medicine, both in the emerging field of molecular epidemiology and in the rational design of new therapeutic agents. The aims of this review are to introduce some of the methods used to construct phylogenetic trees, to illustrate some of the pitfalls that can introduce artifactual results and to speculate on the long-term importance of this area of computational biology in clinical medicine.
Phylogenetic tree selection by the adjusted
Published in Journal of Applied Statistics, 2012
The reconstruction of phylogenetic trees is one of the most important and interesting problems of the evolutionary study. There are many methods proposed in the literature for constructing phylogenetic trees. Each approach is based on different criteria and evolutionary models. However, the topologies of trees constructed from different methods may be quite different. The topological errors may be due to unsuitable criterions or evolutionary models. Since there are many tree construction approaches, we are interested in selecting a better tree to fit the true model. In this study, we propose an adjusted k-means approach and a misclassification error score criterion to solve the problem. The simulation study shows this method can select better trees among the potential candidates, which can provide a useful way in phylogenetic tree selection.
Blood group variation in the Isle of Lewis
Published in Annals of Human Biology, 1985
E.J. Clegg, D. Tills, A. Warlow, J. Wilkinson, A. Marin
Summary Blood groups and protein and enzyme polymorphism distributions were studied in 285 residents on the Isle of Lewis, in the Outer Hebrides. As well as gene frequency calculations for individual loci, genetic distance estimations were made and a phylogenetic tree was constructed. The results indicated several major differences from North-west European populations, with high values of R2(CDe), Rz(CDE) and P1. Among protein and enzyme polymorphisms Hp1, EAPA and PGM11 had very high frequencies. Genetic distances show Lewis to be unlike both Western and Eastern North European populations, while the phylogenetic tree shows a common, but rather distant, ancestry with Icelanders. This genetic uniqueness of Lewis as a whole is accompanied by a considerable degree of heterogeneity within the island itself, especially in the ABO and Rh systems. Stornoway, with a greater proportion of residents descended from immigrant stock, shows a greater degree of similarity with neighbouring populations. The reasons for both the overall uniqueness and the heterogeneity within Lewis are discussed, but in the absence of a large time-depth and adequate vital records, the various roles of selection, drift and migration in producing them are difficult to establish.