We demonstrate that, within this group of closely related animals, there exists a high divergence with regards to traits such as lifespan and stress tolerance and, intriguingly, in the expression of daf-16.
Together the two sequences showed to have a high divergence factor, discriminating almost all mammals.
Among these are a low connectivity, a high divergence and a low path sum.
The chromosomal regions harboring such loci are expected to show reduced variation within lines and also a higher divergence between lines.
While such a high degree of divergence is uncommon for a national collection of self-pollinated landraces, this result is not without precedent; Semagn et al. [ 22] reported a similar mean distance of ~0.35 for a diverse set of CIMMYT maize inbred lines.
All haplotypes sampled from the Indo-Malay-Papua archipelago (IMPA) and the southwestern Pacific coalesced into a clade (clade II) that was deeply separated from a clade grouping all haplotypes from the Persian Gulf and Oman Sea (clade I), and such a high level of genetic divergence suggested the occurrence of two sister species (Fauvelot and Borsa 2012).
Such a high degree of sequence divergence is a very likely explanation supported by previous investigations, which detected an acceleration of substitution rates after the duplication event [ 54- 56].
Contrary to the expectation that genes with such a high level of nucleotide divergence would be undergoing positive selection, the remaining bases are highly conserved and are undergoing purifying selection.
An increase in the substitution rate in plastomes of parasitic plants is a known phenomenon (Bromham et al. 2013), although to our knowledge such high divergence at an intraspecific level has not previously been reported.
Such high divergence among different medaka species re-iterates that a marine transcriptome reference dataset, such as the emerging marine model O. melastigma, is imperative for studies that assess the responses of marine species to pollutants, toxins and stresses at the molecular level.
