The Comparative Method Rules! Codon Volatility Cannot Detect Positive Darwinian Selection Using a Single Genome Sequence

Simple sequence repeats (SSRs) are known as microsatellites, and consist of tandem 1–6-base motifs. They have become one of the most popular molecular markers, and are widely used in molecular ecology, conservation biology, molecular breeding, and many other fields. Previously reported methods identify monomorphic and polymorphic SSRs and determine the polymorphic SSRs via experimental validation, which is potentially time-consuming and costly. Herein, we present a new strategy named insertion/deletion (INDEL) SSR (IDSSR) to identify polymorphic SSRs by integrating SSRs with nucleotide insertions/deletions (INDEL) solely based on a single genome sequence and the sequenced pair-end reads. These INDEL indexes and polymorphic SSRs were identified, as well as the number of repeats, repeat motifs, chromosome location, annealing temperature, and primer sequences, enabling future experimental approaches to determine the correctness and polymorphism. Experimental validation with the giant panda demonstrated that our method has high reliability and stability. The efficient SSR pipeline would help researchers obtain high-quality genetic markers for plants and animals of interest, save labor, and reduce costly marker-screening experiments. IDSSR is freely available at https://github.com/Allsummerking/IDSSR.

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POSITIVE DARWINIAN SELECTION: DOES THE COMPARATIVE METHOD RULE?

Journal of Biological System ◽

10.1142/s0218339007002039 ◽

2007 ◽

Vol 15 (01) ◽

pp. 95-108 ◽

Cited By ~ 7

Author(s):

DONALD R. FORSDYKE

Keyword(s):

Positive Selection ◽

Comparative Method ◽

Positive Darwinian Selection ◽

Stem Loop ◽

Darwinian Selection ◽

Synonymous Mutations ◽

Sequence Method ◽

Internal Forces ◽

Secondary Information ◽

Single Sequence

To detect positive Darwinian selection it is thought essential to compare two sequences. Despite its defects, "the comparative method rules." However, genes evolving rapidly under positive selection conflict more with internal forces (the genome phenotype) than genes evolving slowly under negative selection. In particular, there is conflict with stem-loop potential. The conflict between protein-encoding potential (primary information) and stem-loop potential (secondary information) permits detection of positive selection in a single sequence. The degree to which secondary information is compromised provides a measure of the speed of transmission of primary information. Thus, the sovereignty of the comparative method is challenged not only by its own defects, but also by the availability of a single-sequence method. However, while of limited utility for positive selection, the comparative method casts new light on Darwin's great question — the origin of species. Comparison of rates of synonymous and non-synonymous mutation suggests that branching into new species begins with synonymous mutations.

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