Fig 1.
Population structure of cat breeds via principle component analysis (PCA).
The first two principle components (PC1 and PC2) explain majority of the genetic variation among cat breeds. (a) A broad overview of the population structure of all breeds. Each individual cat is represented by a circle that is colored according to its ancestral group (Western-red, “Middle”-yellow, Eastern-blue) and dashed boxes are used to designate 9 Western breeds (left box), 11 intermediate breeds (middle box) and 6 Eastern breeds (left box). The blue dots extending to the “Middle” and Western groups belong to Bombay breed. Note that Bombay breed is formed by breeding of Burmese and American Shorthair. (b-d) Individual representations of Western, “Middle”, and Eastern breeds, respectively. Note the separation of the interspecies hybrid breed, Bengal, from other “Middle” breeds in (b) and separation of the phenotypically distinct Birman from other Eastern breeds in (c). Six Bombay individuals were outside of the ancestral grouping of Eastern breeds were removed in (d) for ease of presentation.
Fig 2.
The genomic landscape of selection in domestic cat genome.
Chromosomal representation of 205 candidate regions under selection across all cat breeds. Colored vertical bars represent candidate regions under selection and the intensity of color reflects the number of breeds having the particular candidate region. Red, yellow, and blue colored bars correspond to Western (9), “Middle” (11), and Eastern (6) breeds, respectively.
Table 1.
Representative candidate regions under selection in cat breeds with likely phenotype related candidate genes.
Fig 3.
Manhattan plots of genome-wide (di) measures of overlapping 500Kb windows for three cat breeds.
Each dot represents a window of 500 Kb (total 9108 windows) and the horizontal dashed red line indicates the 99th percentile threshold, which distinguishes the top 92 windows. (a) Genome-wide survey of selection for the America Curls, which is a breed defined by backward curled ears. A number of overlapping windows clearly show a signal on Chr. E3. (b) Genome-wide overview of selection for Maine Coon cats, which is a breed recognized by an overall large size and facial features such large oval eyes and a square chin. Visible signals of overlapping windows are shown on Chrs. A1 and A3. (c) Signal of selection for the Turkish Van breed, which is acknowledged for a coat color pattern named after the breed, “Van”. This pattern appears in an overall white coat with distinct coloration in parts of the head and tail. Few overlapping windows were detected on Chrs. A2 and E3. Cat photographs were provided with permission by Larry Johnson.
Fig 4.
Morphological variation in body-form between six Eastern breeds.
Birman symbolizes one extreme end of the physical spectrum of Eastern breeds by displaying stocky body, broad and round head, rounded muzzle, and round eyes whereas Siamese, Oriental, and Peterbald display the other extreme end through a tubular body, wedged head, wedged muzzle, and almond-shaped eyes. Burmese, Bombay exhibit intermediate body-shapes and facial features between the two extremes. Cat photographs were provided with permission by Larry Johnson.