Fig 1.
Phylogeny of species compared in this study.
The figure shows a simplified phylogeny of mice (Mus sp.), rats (Rattus sp.), pouched rats (Cricetomys sp.), and squirrels (Ictidomys sp.). Pouched rats are Nesomyid rodents that are distantly related to Murids. Silhouettes show approximate size differences among species. Time periods are listed along the x-axis, and estimated from previous research [31,32,39]. MYA: million years ago, Plioc: Pliocene, IV: Quaternary period.
Fig 2.
Family-group representation in the pouched rat olfactory receptor gene tree.
Different colors at nodes indicate different families. Colors are repeated within the tree, but similar colors do not indicate similarity of families. All families share > 50% bootstrap support and 40% protein identity.
Fig 3.
Graph comparing functional and pseudogene numbers among select species.
Black bars indicate putatively functional genes and grey bars indicate pseudogenes. Pouched rats, rats, mice, squirrels, dogs, cattle, and pigs have similar numbers of reported olfactory receptor genes. Squirrels have a large number of pseudogenes.
Fig 4.
Comparative gene tree of olfactory receptor sequences for pouched rat, mouse, rat, and squirrel.
Expansions are indicated with group identifiers and arrows. The tree is rooted at the branch separating Class I and Class II receptor clades. The Class I receptor clade is indicated with an open box.
Table 1.
Distribution of pouched rat olfactory receptor genes among subfamilies using a manual pipeline search method [50].
Table 2.
Expanded subfamilies of pouched rat olfactory receptors (ORs) and associated mouse subfamilies.
Fig 5.
Examples of orthologous olfactory receptor (OR) gene sequence among rodents.
Numbers at branch points indicate bootstrap values. A) 1-to-1 orthology between pouched rat, mouse, rat, and squirrel (Ictidomys tridecemilineatus) B) Example of pouched rat paralog within orthologous gene grouping.
Fig 6.
Venn diagram of relative proportions of one-to-one orthology of pouched rat olfactory receptor genes and squirrel, mouse, and rat.
Pouched rats have the largest number of orthologous genes shared with mice and rats. The number of orthologous groupings with squirrels are consistently smaller than orthologies with mice or rats, due to phylogenetic placement.
Table 3.
Distribution of pouched rat olfactory receptors in location clusters.
Table 4.
Pouched rat olfactory receptor (OR) family expansions and numbers of clustered OR sequences within each expansion.