Captive Mexican wolves (Canis lupus baileyi) from two lineages that were kept apart for 15-20 years, McBride and Ghost Ranch, and wolves from the crosses made after the lineages were merged in 1995: first-generation crosses (F1), first backcrosses to McBride and second backcrosses to McBride. A young hybrid population with a known pedigree for every animal.
Format
A list with:
- genotypes
Integer matrix, 56 wolves x 486 SNPs, counting Ghost Ranch (species 2) alleles (0, 1, 2;
NAmissing). The SNPs are fixed between the two reference groups and typed in every reference wolf, and are spread over the 38 autosomes in proportion to their length.- groups
Group of each wolf:
"ref1"(pure McBride, 31),"ref2"(pure Ghost Ranch, 6),"F1"(5),"BC1_MB"(11) and"BC2_MB"(3).- map
Data frame with
snp,chromosome,position(cM, approximate: Mb x 0.97, the genome-wide rate of the dog linkage map) andbp(CanFam2).- truth
Data frame, one row per group:
group,n,class(as named byclassify_hybrids()),descriptionandhybrid_age.- animals
Data frame, one row per wolf:
id,group,classandhybrid_agefrom the pedigree.- description
A short description.
Source
Data package of Fitak et al. (2018) on Dryad,
doi:10.5061/dryad.g68k008
(files MW.ped and MW.map). CC0 1.0.
Truth
Every wolf's class comes from the pedigree and was checked against its
genotypes. Hybrid age is the number of generations back to the nearest
pure ancestor, averaged over the pedigree lines: F1 = 1, first backcross
= 1.5, second backcross = 1.75. The sample labelled "547" is a
re-identified museum voucher and is an F1. The two lineages differ only
by drift from very few founders, the Ghost Ranch reference is only six
related wolves (including parents of the hybrids), and several hybrids are
full siblings. With at most two meioses since the F1, ancestry blocks are
long, so markers on one chromosome are far from independent (see
effective_markers()).
Licence
The genotypes are from Dryad and were released under CC0 1.0 (public domain dedication). They were subset to the markers and wolves described above and recoded.
References
Fitak RR, Rinkevich SE, Culver M (2018) Genome-wide analysis of SNPs is consistent with no domestic dog ancestry in the endangered Mexican wolf (Canis lupus baileyi). Journal of Heredity. doi:10.1093/jhered/esy009
Examples
mk <- diagnostic_markers(wolves$genotypes, wolves$groups, "ref1", "ref2")
sc <- hybrid_scores(wolves$genotypes, mk)
cl <- classify_hybrids(sc)
table(truth = wolves$animals$class, called = cl$class)
#> called
#> truth BC1_species1 BC2_species1 F1 pure1 pure2
#> BC1_species1 11 0 0 0 0
#> BC2_species1 0 3 0 0 0
#> F1 0 0 5 0 0
#> pure1 0 0 0 31 0
#> pure2 0 0 0 0 6