Background Information
| Breed Card | |
| Breed | Ceylon Jungle Fowl |
| Species taxonomy | Gallus lafayetii |
| Classification | Ceylon Jungle Fowl |
| Region | Sri Lanka |
| Purpose | Ceylon Jungle Fowl |
The Celyon Jungle Fowl (Gallus lafayettii), also known as the Sri Lankan Jungle Fowl, is endemic to Sri Lanka, where it is the national bird. The specific name of the Ceylon Jungle Fowl commemorates the French aristocrat Gilbert du Motier, marquis de La Fayette.
As with other junglefowl, the Celyon Jungle Fowl is sexually dimorphic: the male is larger than the female, with more vivid plumage and a highly exaggerated wattle and comb. The male Celyon Jungle Fowl ranges from 66-72 cm (26-28 in) in length, and 790-1,140 g (1.74-2.51 lb) in weight. The male has orange-red body plumage, and dark purple to black wings and tail. The feathers of the mane descending from head to base of spine are golden, and the face has bare red skin and wattles. The comb is red with a yellow centre. As with the green junglefowl, the male does not possess an eclipse plumage.The female is much smaller, at only 35 cm (14 in) in length and 510-645 g (1.124-1.422 lb) in weight, with dull brown plumage with white patterning on the lower belly and breast, ideal camouflage for a nesting bird.
Variants Annotation&Density
| Annotation | Population SNP | Total SNP | Percentage SNP | Population INDEL | Total INDEL | Percentage INDEL |
|---|---|---|---|---|---|---|
| downstream | 67965 | 650455 | 10.4488% | 8252 | 104154 | 7.9229% |
| exonic;splicing | 9 | 188 | 4.7872% | 0 | 0 | 0% |
| exonic_unknown | 26 | 582 | 4.4674% | 0 | 82 | 0% |
| frameshift_deletion | 0 | 0 | 0% | 545 | 15977 | 3.4112% |
| frameshift_insertion | 0 | 0 | 0% | 380 | 13308 | 2.8554% |
| intergenic | 1509623 | 15129055 | 9.9783% | 162343 | 2238383 | 7.2527% |
| intronic | 1847473 | 17735594 | 10.4168% | 210017 | 2641780 | 7.9498% |
| ncRNA_exonic | 40831 | 400185 | 10.203% | 3959 | 54342 | 7.2853% |
| ncRNA_exonic;splicing | 23 | 231 | 9.9567% | 4 | 43 | 9.3023% |
| ncRNA_intronic | 364052 | 3728327 | 9.7645% | 41490 | 575920 | 7.2041% |
| ncRNA_splicing | 237 | 2341 | 10.1239% | 31 | 478 | 6.4854% |
| ncRNA_UTR5 | 0 | 0 | 0% | 1 | 18 | 5.5556% |
| nonframeshift_deletion | 0 | 0 | 0% | 396 | 8777 | 4.5118% |
| nonframeshift_insertion | 0 | 0 | 0% | 161 | 4784 | 3.3654% |
| nonsynonymous | 21271 | 336233 | 6.3263% | 0 | 0 | 0% |
| splice_acceptor | 29 | 750 | 3.8667% | 37 | 964 | 3.8382% |
| splice_donor | 59 | 1076 | 5.4833% | 18 | 763 | 2.3591% |
| splice_donor_acceptor | 0 | 0 | 0% | 0 | 45 | 0% |
| splice_UTR5 | 38 | 400 | 9.5% | 8 | 106 | 7.5472% |
| splie_Others | 0 | 0 | 0% | 22 | 654 | 3.3639% |
| startloss | 67 | 671 | 9.9851% | 0 | 51 | 0% |
| stopgain | 265 | 4175 | 6.3473% | 20 | 1252 | 1.5974% |
| stoploss | 28 | 353 | 7.932% | 0 | 63 | 0% |
| synonymous | 43407 | 548813 | 7.9093% | 0 | 0 | 0% |
| upstream | 72672 | 679592 | 10.6935% | 8118 | 98760 | 8.2199% |
| upstream;downstream | 5998 | 57451 | 10.4402% | 728 | 9367 | 7.772% |
| UTR3 | 35506 | 361040 | 9.8344% | 4640 | 61415 | 7.5552% |
| UTR5 | 10264 | 112990 | 9.084% | 1065 | 16935 | 6.2888% |
| UTR5;UTR3 | 258 | 2524 | 10.2219% | 27 | 381 | 7.0866% |
| Total | 4020101 | 39753026 | 10.1127% | 442262 | 5848802 | 7.5616% |
Genetic Differentiation
Summary
Genetic affinities of target population in the context of worldwide populations are measured by pairwise FST between target population and references. Smaller FST value indicates closer relationship. Regions represented by different colors are indicated above.
Genetic Affinity
Summary
Genetic affiliation and population structure are shown by PCA plots. After removing G. g. bankiva, G. g. jabouillei, and some G. g. gallus individuals as outliers to other Red Jungle Fowl, the dataset contains 1,915 samples from domestic chicken and Red Jungle Fowl. User can add any populations with interests to show with the target population under this PCA context by using the item of “Add”.
ADMIXTURE Analysis
Summary
The inference of populations and individual ancestries is revealed by ADMIXTURE clustering. Length of each colored bar represents the proportion of proposed ancestry in the sample. User can add any populations with interests to compare with the target population by using the item of “Add”. The number of proposed ancestries is determined by “which K”.
Runs of Homozygosity
Summary
Runs of homozygosity (ROH) indicates long tracts of homozygous genotypes inherited from identical haplotypes of a common ancestor. Larger populations have fewer, shorter ROH, whereas isolated or bottlenecked populations have more, somewhat longer ROH. Admixture brings the fewest ROH, whereas inbreeding causes long ROH. The level of ROH is measured by number and length. The length of ROH can be defined in “ROH range”. User can add any populations with interests to compare with the target population by using the item of “Add”.
Linkage Disequilibrium Decay
Summary
Linkage disequilibrium (LD) decay is characterized by squared correlations (r²) of all SNPs frequencies against the physical distances between SNPs. User can add any populations with interests to compare with the target population by using the item of “Add”.
Demographic History
Summary
The changes of effective population size through time is inferred by SMC++. User can add any populations with interests to compare with the target population by using the item of “Add”.
Selection
Summary
Selective signals of the target population are detected by different methods. X axis indicates physical position of specific chromosomal region with interests which can be defined by “Region”. The gene annotation is shown below. Y axis of left (YL) indicates the values of Pi-ratio of -log2(πRJF/πTarget) or composite likelihood ratio (CLR) of SweeD. The levels of statistical significance are noted with different colors. Y axis of right (YR) shows the values of Fst (Target vs. Red Jungle Fowl), Pi, or Tajima’s D with blue line with sliding window approach. The genomic window size and step size for Tajima’s D are 5 kb and 5 kb, respectively. The genomic window size and step size for Fst and Pi are 10 kb and 5 kb, respectively. The methods are defined by “Method-YL” and “Method-YR”.
