Current Released Version:
1.2 (October, 2006)
satDNA Analyzer (satellite-DNA Analyzer), is a software package for the
analysis of satellite-DNA sequences from aligned DNA sequence data. It
allows for the analysis
of the patterns of variation at each nucleotide position considered independently
amongst all units of a given satellite-DNA family when comparing two species.
The program classifies each site accordingly as monomorphic or polymorphic, discriminates shared from non-shared
polymorphisms and classifies each non-shared polymorphism according to the
model proposed by
Strachan et al. (1985)
in six different
stages of transition during the spread of a variant repeat unit toward its
fixation. Furthermore, this program implements several other utilities for
satellite-DNA analysis evolution such as the design of the average consensus
sequences, the average base pair contents, the distribution of variant sites,
the transition to transversion
rate, and different
estimates of intra and inter-specific variation.
Aprioristic hypotheses on factors influencing the
molecular drive process and the rates and biases of concerted evolution can
be tested with this program. Additionally, satDNA
Analyzer generates an output file containing an alignment to be used for further
evolutionary analysis by using different phylogenetic
. The novelty of this feature is that it
allows to discard
the shared polymorphisms for the
analysis, which we have demonstrated can interfere with the results when analyzing
closely related species (Navajas-Perez
et al., 2005
satDNA Analyzer Features
1.- Sequence Translator
satDNA Analyzer reads and outputs most common sequence
software uses the SEQIO.
- J. Knight (1996). SEQIO: A Package for Reading and Writing Sequence Files, distributed by the author.
2.- Transition-Stages Finder
The program recognizes different positions and transition stages, according to the following
- Non-monomorphic positions: POLYMORPHISM:
- Both species share at least two nucleotides: Shared polymorphism.
- Both species share up to one nucleotide: Non-shared polymorphisms sensu lato.
- No fixed positions in any species: Irrelevant positions.
- One fixed position: Variable Transition States (VTS).
- Indels included: Irrelevant positions with indels.
- No indels: Strachan Transition States (STS):
- STS-II: mutation in one species spread up to 25% of sequences.
- STS-III: mutation in one species spread between 25-50% of sequences.
- STS-IV: mutation in one species spread between 50-100% of sequences.
- STS-V: different nucleotides fixed in each species.
- STS-VI: a new cycle of mutation-homogenization starts.
- Monomorphic position: STS I.
3.- Estimates of DNA Divergence Between Species
The program estimates the following measures for each individual species:
- The average number of nucleotide differences (Tajima 1983, equation A3).
- The nucleotide diversity, Pi (Nei 1987 equation 10.5).
- Nucleotide diversity with Jukes and Cantor, Pi (JC) (Nei 1987, equations 10.19 and 5.3; Lynch and Crease 1990, equations 1-2).
And considering the two species:
- The average number of nucleotide substitutions per site between species, Dxy (Nei 1987, equation 10.20).
- Dxy with Jukes and Cantor (Nei 1987, equation 10.20 using the Jukes and Cantor correction).
- The number of net nucleotide substitutions per site between species, Da (Nei 1987, equation 10.21).
- Da with Jukes and Cantor (Nei 1987, equation 10.21 using the Jukes and Cantor correction).
If the rate of nucleotide substitution is constant and is Ī» per site per year and the time since divergence between the two speices is T, then users are able to estimate the expected value of Da by the equation 10.22 (Nei 1987).
- The proportions of transitional differences (P) and transversional differences (Q) and the ratio of transitional to transversional differences (Rd).
- Lynch, M. & Crease, T J. (1990). The analysis of population survey data on DNA sequence variation. Mol. Biol. Evol., 7:377-394.
- Nei, M. (1987). Molecular Evolutionary Genetics. Columbia University Press, New York, NY.
- Tajima, F. (1983). Evolutionary relationship of DNA sequences in finite populations. Genetics, 105:437-460.
4.- Removing shared polymorphisms from alignment
SatDNA Analyzer generates an output file alingment without shared
polymorphisms to be used in further phylogenetic analysis. We have
recently proposed a model for the analysis of satellite-DNA sequences
of closely related species (Navajas-Perez et al., 2005). We propose
there that shared polymorphisms are ancestral variation prior to species
spliting and therefore they could interfere with the results. In contrast,
nonshared polymophisms are automorphies, representing different transitional
stages in the proccess of intraspecific sequence homogenization and
interspecific divergence. So, shared polymorphisms should be excluded
in some cases from the alignment to allow more accurate calculations.
- R. Navajas-Pérez, R. de la Herrán, C. Ruiz Rejón, M. Jamilena,
R. Lozano, C. Ruiz Rejón, M. Ruiz Rejón & M. A. Garrido-Ramos (2005). Reduced rates of sequence evolution of Y-linked satellite DNA in Rumex (Polygonaceae). J. Mol. Evol. (2005) 60:391-399