"In biology, phylogenetics is the study of the evolutionary history and relationships among or within groups of organisms."
The study of the evolutionary history of organisms and their relationships to one another.
Taxonomy: Classification of organisms based on their characteristics.
Systematics: Study of diversification and relationships of different organisms.
Phylogeny: Evolutionary history of a group of organisms.
Molecular evolution: Evolutionary changes at the molecular level.
Homology: The similarity in structure or sequence of genes or proteins indicates common ancestry.
Paralogy: Similarity between genes or proteins that have arisen from gene duplication events.
Orthology: Similarity between genes or proteins that occur after speciation.
Markers: Molecular sequences used to distinguish lineages in phylogenetic analysis.
Tree construction: Methods of inferring evolutionary relationships between organisms.
Maximum Parsimony: A tree-building approach that selects the evolutionary tree with the fewest number of changes.
Maximum Likelihood: A statistical approach that finds the most probable tree given the data.
Bayesian Inference: A probabilistic approach that takes into account prior knowledge and finds the most probable tree given the data and prior knowledge.
Distance-based methods: A tree-building approach that calculates the evolutionary distances between sequences and constructs the tree based on those distances.
Consensus trees: A method of constructing a tree from multiple trees obtained by different methods.
Molecular clocks: A method of estimating the time of divergence between species based on the rate of evolution of molecular sequences.
Co-evolution: The evolution of one species in response to the evolution of another species with which it interacts.
Phylogeography: The study of the historical processes that have shaped the geographic distribution of species.
Comparative methods: The comparison of traits across different species to understand their evolutionary significance.
Cladistics: A method of classification that groups organisms based on shared derived characteristics. The goal is to create a tree-like diagram called a cladogram, which shows the relationships between different groups of organisms.
Ancestral State Reconstruction: The process of inferring the ancestral states of characters or traits in a phylogenetic tree. This can be useful for understanding the evolution of certain traits and how they may have changed over time.
Molecular Phylogenetics: A type of phylogenetics that uses genetic data, such as DNA or RNA sequences, to infer evolutionary relationships between organisms. This can provide insight into the relatedness of organisms at the molecular level.
Biogeography: The study of how organisms have evolved and spread across different geographic regions. This type of phylogenetics can help us understand the history of different populations and how they came to be distributed in different locations.
Paleontology: The study of fossils and their use in understanding the history of life on Earth. Paleontologists can use phylogenetics to understand the relationships between different extinct and living organisms.
Phylogeography: The study of the geographic distribution of genetic lineages and how they have been shaped by historical events, such as changes in climate or biogeographical barriers.
Phylogenomics: An approach that integrates molecular data from multiple genes or genomes to construct phylogenetic trees. This can provide a more comprehensive view of evolutionary relationships than using a single gene or molecular marker.
Phyloinformatics: The use of computational tools to analyze and visualize phylogenetic data. This can include programs for constructing and interpreting phylogenetic trees, as well as tools for exploring and analyzing large datasets of genetic or morphological data.
Comparative Anatomy: The study of similarities and differences in the structure and function of different organisms. Comparative anatomy can be used to infer evolutionary relationships and understand the origins of different traits.
Evolutionary Developmental Biology (Evo-Devo): The study of how genetic and developmental processes contribute to the evolution of different organisms. This type of phylogenetics can help us understand how changes in development have led to the diversity of life we see today.
"These relationships are determined by phylogenetic inference methods that focus on observed heritable traits, such as DNA sequences, protein amino acid sequences, or morphology."
"The result of such an analysis is a phylogenetic tree—a diagram containing a hypothesis of relationships that reflects the evolutionary history of a group of organisms."
"The tips of a phylogenetic tree can be living taxa or fossils, and represent the 'end' or the present time in an evolutionary lineage."
"A rooted tree diagram indicates the hypothetical common ancestor of the tree. An unrooted tree diagram (a network) makes no assumption about the ancestral line, and does not show the origin or 'root' of the taxa in question or the direction of inferred evolutionary transformations."
"Such uses have become central to understanding biodiversity, evolution, ecology, and genomes."
"Phylogenetics is a component of systematics that uses similarities and differences of the characteristics of species to interpret their evolutionary relationships and origins."
"In the field of cancer research, phylogenetics can be used to study the clonal evolution of tumors and molecular chronology, predicting and showing how cell populations vary throughout the progression of the disease and during treatment."
"The evolutionary processes behind cancer progression are quite different from those in species and are important to phylogenetic inference; these differences manifest in at least four areas: the types of aberrations that occur, the rates of mutation, the intensity, and high heterogeneity - variability - of tumor cell subclones."
"Phylogenetics allows scientists to organize species and can show which species are likely to have inherited particular traits that are medically useful, such as producing biologically active compounds."
"For example, in drug discovery, venom-producing animals are particularly useful. Venoms from these animals produce several important drugs, e.g., ACE inhibitors and Prialt (Ziconotide)."
"In forensic science, phylogenetic tools are useful to assess DNA evidence for court cases."
"HIV forensics uses phylogenetic analysis to track the differences in HIV genes and determine the relatedness of two samples."
"HIV forensics does have its limitations, i.e., it cannot be the sole proof of transmission between individuals and phylogenetic analysis, which shows transmission relatedness, does not indicate direction of transmission."