A patrocladogram is a

cladistic Cladistics (; ) is an approach to biological classification in which organisms are categorized in groups ("clades") based on hypotheses of most recent common ancestry. The evidence for hypothesized relationships is typically shared derived char ...

branching pattern that has been precisely modified by use of patristic distances (i.e., divergences between lineages); a type of phylogram. The patristic distance is defined as, "the number of apomorphic step changes separating two taxa on a cladogram," and is used exclusively to determine the amount of divergence of a characteristic from a common ancestor. This means that cladistic and patristic distances are combined to construct a new tree using various phenetic

algorithms In mathematics and computer science, an algorithm () is a finite sequence of rigorous instructions, typically used to solve a class of specific problems or to perform a computation. Algorithms are used as specifications for performing ...

. The purpose of the patrocladogram in

biological classification In biology, taxonomy () is the scientific study of naming, defining ( circumscribing) and classifying groups of biological organisms based on shared characteristics. Organisms are grouped into taxa (singular: taxon) and these groups are give ...

is to form a hypothesis about which evolutionary processes are actually involved before making a taxonomic decision. Patrocladograms are based on biostatistics that include but are not limited to: parsimony,

distance matrix In mathematics, computer science and especially graph theory, a distance matrix is a square matrix (two-dimensional array) containing the distances, taken pairwise, between the elements of a set. Depending upon the application involved, the ''dist ...

, likelihood methods, and

Bayesian probability Bayesian probability is an interpretation of the concept of probability, in which, instead of frequency or propensity of some phenomenon, probability is interpreted as reasonable expectation representing a state of knowledge or as quantification ...

. Some examples of genomically related

data In the pursuit of knowledge, data (; ) is a collection of discrete Value_(semiotics), values that convey information, describing quantity, qualitative property, quality, fact, statistics, other basic units of meaning, or simply sequences of sy ...

that can be used as inputs for these methods are: molecular sequences, whole

genome In the fields of molecular biology and genetics, a genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding g ...

sequences, gene frequencies,

restriction site Restriction sites, or restriction recognition sites, are located on a DNA molecule containing specific (4-8 base pairs in length) sequences of nucleotides, which are recognized by restriction enzymes. These are generally palindromic sequences (bec ...

s, distance matrices, unique characters, mutations such as

SNPs In genetics, a single-nucleotide polymorphism (SNP ; plural SNPs ) is a germline substitution of a single nucleotide at a specific position in the genome. Although certain definitions require the substitution to be present in a sufficiently larg ...

, and

mitochondrial genome Mitochondrial DNA (mtDNA or mDNA) is the DNA located in mitochondria, cellular organelles within eukaryotic cells that convert chemical energy from food into a form that cells can use, such as adenosine triphosphate (ATP). Mitochondrial ...

data.

Cautions with patrocladogram usage

Patrocladograms are graphs that assert hypotheses of similarity whereas

phylogenetic In biology, phylogenetics (; from Greek φυλή/ φῦλον [] "tribe, clan, race", and wikt:γενετικός, γενετικός [] "origin, source, birth") is the study of the evolutionary history and relationships among or within groups o ...

trees are graphs that assert hypotheses of common ancestry. When a patrocladogram does not logically match with a comparable phylogenetic tree hypothesis it should not be used to define monophyletic groups. The usage of patrocladograms can skew interpretations of novel evolution or depict homologous traits as

homoplastic Homoplasy, in biology and phylogenetics, is the term used to describe a Phenotypic trait, feature that has been gained or lost independently in separate lineages over the course of evolution. This is different from Homology (biology), homology, wh ...

Programs for patrocladogram analysis

Most phylograms are saved in some variant of the

Newick format In mathematics, Newick tree format (or Newick notation or New Hampshire tree format) is a way of representing graph-theoretical trees with edge lengths using parentheses and commas. It was adopted by James Archie, William H. E. Day, Joseph Fels ...

such as:

PAUP* PAUP* (Phylogenetic Analysis Using Parsimony *and other methods) is a computational phylogenetics program for inferring evolutionary trees (Phylogenetics, phylogenies), written by David L. Swofford. Originally, as the name implies, PAUP only implem ...

MEGA, Molecular Evolutionary Genetics Analysis Molecular Evolutionary Genetics Analysis (MEGA) is computer software for conducting statistical analysis of molecular evolution and for constructing phylogenetic trees. It includes many sophisticated methods and tools for phylogenomics and phyl ...

Clustal Clustal is a series of widely used computer programs used in bioinformatics for multiple sequence alignment. There have been many versions of Clustal over the development of the algorithm that are listed below. The analysis of each tool and its ...

PHYLIP PHYLogeny Inference Package (PHYLIP) is a free computational phylogenetics package of programs for inferring evolutionary trees (Phylogenetics, phylogenies). It consists of 65 Porting, portable programs, i.e., the source code is written in the prog ...

, or

Nexus file The extensible NEXUS file format is widely used in bioinformatics. It stores information about taxa, morphological and molecular characters, distances, genetic codes, assumptions, sets, trees, etc. Several popular phylogenetic programs such as PA ...

. These various versions of the Newick format can then be used as an input for patristic distances in patrocladogram formation. There are two widely used pieces of

software Software is a set of computer programs and associated software documentation, documentation and data (computing), data. This is in contrast to Computer hardware, hardware, from which the system is built and which actually performs the work. ...

; one is used for

analyzing Analysis (plural, : analyses) is the process of breaking a complexity, complex topic or Substance theory, substance into smaller parts in order to gain a better understanding of it. The technique has been applied in the study of mathematics a ...

patristic distance, and the other for creating a viewable patrocladogram. See both programs below:

PATRISTIC

Patristic is a Java program that uses different tree files as input and computes their patristic distances. Patristic allows saving and editing those distances. Patristic provides different graphic views of the results as well as the possibility to save them in the CSV format for building graphics using Excel.

RAMI

RAMI uses branch lengths to create clusters which can then be visualized as a patrocladogram.

References

External links