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Retrotransposon markers are retrotransposon
Retrotransposon

Retrotransposons are Genetics elements that can amplify themselves in a genome and are ubiquitous components of the DNA of many Eukaryote organisms....
s that are used as cladistic
Cladistics

Cladistics is the hierarchical classification of species based on evolutionary ancestry. Cladistics is distinguished from other taxonomic systems because it focuses on evolution rather than similarities between species, and because it places heavy emphasis on objective, quantitative analysis....
 markers.

The analysis of SINE
Retrotransposon

Retrotransposons are Genetics elements that can amplify themselves in a genome and are ubiquitous components of the DNA of many Eukaryote organisms....
s – Short INterspersed Elements – LINE
Retrotransposon

Retrotransposons are Genetics elements that can amplify themselves in a genome and are ubiquitous components of the DNA of many Eukaryote organisms....
s – Long INterspersed Elements – or truncated LTR
Retrotransposon

Retrotransposons are Genetics elements that can amplify themselves in a genome and are ubiquitous components of the DNA of many Eukaryote organisms....
s – Long Terminal Repeats – as molecular cladistic
Cladistics

Cladistics is the hierarchical classification of species based on evolutionary ancestry. Cladistics is distinguished from other taxonomic systems because it focuses on evolution rather than similarities between species, and because it places heavy emphasis on objective, quantitative analysis....
 markers represents a particularly interesting complement to DNA sequence
DNA sequence

A DNA sequence or genetic sequence is a succession of letters representing the primary structure of a real or hypothetical DNA molecule or strand, with the capacity to carry information as described by the central dogma of molecular biology....
 and morphological
Morphology (biology)

The term morphology in biology refers to form, structure and configuration of an organism. This includes aspects of the outward appearance as well as the form and structure of the internal parts like bones and organs....
 data. The reason for this is that retrotransposons are assumed to represent powerful noise-poor synapomorphies (Shedlock and Okada, 2000).






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Retrotransposon markers are retrotransposon
Retrotransposon

Retrotransposons are Genetics elements that can amplify themselves in a genome and are ubiquitous components of the DNA of many Eukaryote organisms....
s that are used as cladistic
Cladistics

Cladistics is the hierarchical classification of species based on evolutionary ancestry. Cladistics is distinguished from other taxonomic systems because it focuses on evolution rather than similarities between species, and because it places heavy emphasis on objective, quantitative analysis....
 markers.

The analysis of SINE
Retrotransposon

Retrotransposons are Genetics elements that can amplify themselves in a genome and are ubiquitous components of the DNA of many Eukaryote organisms....
s – Short INterspersed Elements – LINE
Retrotransposon

Retrotransposons are Genetics elements that can amplify themselves in a genome and are ubiquitous components of the DNA of many Eukaryote organisms....
s – Long INterspersed Elements – or truncated LTR
Retrotransposon

Retrotransposons are Genetics elements that can amplify themselves in a genome and are ubiquitous components of the DNA of many Eukaryote organisms....
s – Long Terminal Repeats – as molecular cladistic
Cladistics

Cladistics is the hierarchical classification of species based on evolutionary ancestry. Cladistics is distinguished from other taxonomic systems because it focuses on evolution rather than similarities between species, and because it places heavy emphasis on objective, quantitative analysis....
 markers represents a particularly interesting complement to DNA sequence
DNA sequence

A DNA sequence or genetic sequence is a succession of letters representing the primary structure of a real or hypothetical DNA molecule or strand, with the capacity to carry information as described by the central dogma of molecular biology....
 and morphological
Morphology (biology)

The term morphology in biology refers to form, structure and configuration of an organism. This includes aspects of the outward appearance as well as the form and structure of the internal parts like bones and organs....
 data. The reason for this is that retrotransposons are assumed to represent powerful noise-poor synapomorphies (Shedlock and Okada, 2000). The target sites
Retrotransposon

Retrotransposons are Genetics elements that can amplify themselves in a genome and are ubiquitous components of the DNA of many Eukaryote organisms....
 are relatively unspecific so that the chance of an independent integration of exactly the same element into one specific site in different taxa is not large and may even be negligible over evolutionary time scales. Retrotransposon integrations are currently assumed to be irreversible events; this might change since no eminent biological mechanisms
Biological process

A biological process is a process of a living organism. Biological processes are made up of any number of chemical reactions or other events that results in a Chemical transformation....
 have yet been described for the precise re-excision of class I transposon
Transposon

Transposons are sequences of DNA that can move around to different positions within the genome of a single cell , a process called transposition....
s, but see van de Lagemaat et al. (2005). A clear differentiation between ancestral and derived
Derived

In phylogenetics, a trait is derived if it is present in an organism, but was absent in the last common ancestor of the group being considered. This may also refer to structures that are not present in an organism, but were present in its ancestors, i.e. traits that have undergone secondary loss....
 character state at the respective locus
Locus (genetics)

In the fields of genetics and evolutionary computation, a locus is a fixed position on a chromosome such as the position of a genetic marker that may be occupied by one or more genes....
 thus becomes possible as the absence of the introduced sequence can be with high confidence considered ancestral.

In combination, the low incidence of homoplasy together with a clear character polarity make retrotransposon integration markers ideal tools for determining the common ancestry of taxa by a shared derived
Derived

In phylogenetics, a trait is derived if it is present in an organism, but was absent in the last common ancestor of the group being considered. This may also refer to structures that are not present in an organism, but were present in its ancestors, i.e. traits that have undergone secondary loss....
 transpositional event (Hamdi et al. 1999; Shedlock and Okada 2000). The “presence” of a given retrotransposon in related taxa suggests their orthologues integration, a derived
Derived

In phylogenetics, a trait is derived if it is present in an organism, but was absent in the last common ancestor of the group being considered. This may also refer to structures that are not present in an organism, but were present in its ancestors, i.e. traits that have undergone secondary loss....
 condition acquired via a common ancestry, while the “absence” of particular elements indicates the plesiomorphic condition prior to integration in more distant taxa. The use of presence/absence analyses to reconstruct the systematic biology
Cladistics

Cladistics is the hierarchical classification of species based on evolutionary ancestry. Cladistics is distinguished from other taxonomic systems because it focuses on evolution rather than similarities between species, and because it places heavy emphasis on objective, quantitative analysis....
 of mammal
Mammal

Mammals are a class of vertebrate animals whose name is derived from their distinctive feature, mammary glands, with which they feed their young....
s depends on the availability of retrotransposons that were actively integrating before the divergence of a particular species
Species

In biology, a species is one of the basic units of biological classification and a taxonomic rank. A species is often defined as a group of organisms capable of interbreeding and producing fertile offspring....
.

Examples for phylogenetic studies based on retrotransposon presence/absence data are the definition of whales as members of the order Cetartiodactyla
Cetartiodactyla

Cetartiodactyla is the clade to which whales and even-toed ungulates have currently been placed. The term was coined by merging the name for the two orders, Cetacea and Artiodactyla, into a single word....
 with hippos being their closest living relatives (Nikaido et al., 1999), hominoid relationships (Salem et al. 2003), the Strepsirrhine tree (Roos et al., 2004) and the placental mammalian evolution (Kriegs et al., 2006).

Inter-Retrotransposons Amplified Polymorphisms (IRAPs) are an alternative valuable retrotransposon-based markers. In this method, PCR oligonucleotide primers facing outwards from the LTR or other regions of retrotransposons are made and amplify between two retroelements inserted into the genome. As discussed above, the insertion of elements into the genome mean that the number of sites amplified and sizes of inter-retroelement fragments differ between different lines, and can be used as markers to detect genotypes, measure diversity or reconstruct phylogeny (see Flavell et al. 1999; Kalendar et al. 1999; Kumar & Hirochika 2001).