CR1 retroposons provide a new insight into the phylogeny of Phasianidae species (Aves: Galliformes)

Chicken repeat 1 (CR1) elements, a class of retroposons belonging to non-long-terminal repeats, have been recognized as powerful tools for phylogenetic studies. Here we examine the phylogenetic relationships of 11 Phasianidae species based on CR1 retroposons. Together with 19 loci reported previously, a total of 99 CR1 loci were identified from chicken genome and turkey BAC clone sequences. 75 insertion events were used to address the branching order of 11 species in Phasianidae. The topology of our tree suggests that: 1) Gallus gallus possessed a basal phylogenetic position within Phasianidae and was related to Bambusicola thoracica (BSP = 100%); 2) After the split of G. gallus and B. thoracica, Arborophila rufipectus diverged from Phasianidae (BSP = 100%). Nine unambiguous insertion events supported a phylogenetic position of A. rufipectus different to previous mitochondrial data suggesting a hybrid origin or an ancient introgression of A. rufipectus; and 3) 22 CR1 insertion events strongly supported the eight phasianids under investigation sharing a common ancestor. Our study has revisited the phylogenetic position of G. gallus and A. rufipectus and provided a new insight into the phylogeny of Phasianidae birds. It showed that a CR1-based methodology has a great potential to be informative within Phasianidae in resolving relationships of closely related species whose radiation and speciation have occurred very recently.

► Phylogeny of Phasianidae was constructed based on CR1 with robust supports.
► Gallus gallus possessed a basal phylogenetic position within Phasianidae.
► G. gallus was related to Bambusicola thoracica.
► Arborophila rufipectus diverged after the split of G. gallus and B. thoracica.
► 22 CR1 loci support the other eight phasianids sharing a common ancestor.