A patrocladogram is a

cladistic Cladistics ( ; from Ancient Greek 'branch') 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 ...

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 mathematically rigorous instructions, typically used to solve a class of specific problems or to perform a computation. Algorithms are used as specifications for per ...

. 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 Biostatistics (also known as biometry) is a branch of statistics that applies statistical methods to a wide range of topics in biology. It encompasses the design of biological experiments, the collection and analysis of data from those experimen ...

that include but are not limited to: parsimony, distance matrix, likelihood methods, and

Bayesian probability Bayesian probability ( or ) 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 quant ...

. Some examples of genomically related

data Data ( , ) are a collection of discrete or continuous values that convey information, describing the quantity, quality, fact, statistics, other basic units of meaning, or simply sequences of symbols that may be further interpreted for ...

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

genome 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 genes, other functional regions of the genome such as ...

sequences, gene frequencies,

restriction site In molecular biology, restriction sites, or restriction recognition sites, are regions of a DNA molecule containing specific (4-8 base pairs in length) sequences of nucleotides; these are recognized by restriction enzymes, which cleave the DNA at ...

s, distance matrices, unique characters, mutations such as

SNPs In genetics and bioinformatics, 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 ...

, and mitochondrial genome data.

Cautions with patrocladogram usage

Patrocladograms are graphs that assert

hypotheses A hypothesis (: hypotheses) is a proposed explanation for a phenomenon. A scientific method, scientific hypothesis must be based on observations and make a testable and reproducible prediction about reality, in a process beginning with an educ ...

of similarity whereas

phylogenetic In biology, phylogenetics () is the study of the evolutionary history of life using observable characteristics of organisms (or genes), which is known as phylogenetic inference. It infers the relationship among organisms based on empirical dat ...

trees are graphs that assert hypotheses of common

ancestry An ancestor, also known as a forefather, fore-elder, or a forebear, is a parent or ( recursively) the parent of an antecedent (i.e., a grandparent, great-grandparent, great-great-grandparent and so forth). ''Ancestor'' is "any person from ...

. 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.

Programs for patrocladogram analysis

Most phylograms are saved in some variant of the Newick format such as: PAUP*, MEGA, Molecular Evolutionary Genetics Analysis, Clustal, PHYLIP, or

Nexus file The extensible NEXUS file format is widely used in phylogenetics, evolutionary biology, and bioinformatics. It stores information about taxa In biology, a taxon (back-formation from ''taxonomy''; : taxa) is a group of one or more population ...

. 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 consists of computer programs that instruct the Execution (computing), execution of a computer. Software also includes design documents and specifications. The history of software is closely tied to the development of digital comput ...

; one is used for analyzing 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