Fig. 4.

Phylogenetic affiliations of Laonastes based on presence/absence patterns of retroposed SINEs. The phylogenetic tree indicates the three major rodent clades: the mouse-related clade, the Ctenohystrica, and the squirrel-related clade. Eleven retroposed elements, present in certain mouse-related species (blue circles), were clearly absent in Laonastes. Nine other SINEs, present in certain Hystricognathi species (orange circles), were also absent in Laonastes. The monophyly marker of Ctenohystrica was present in all representatives including Laonastes (black circle) and was absent in members of both the mouse- and squirrel-related clades. Four diagnostic markers were present in Laonastes and Ctenodactylus (red circles) but absent in all other investigated rodents. Detailed information on the 11 investigated loci and diagnostic SINE markers are given in SI Appendix.