Burrowing bettongs, or boodies (Bettongia lesueur), from two subspecies were released together into a predator-proof fenced reserve in Western Australia in 2010: animals from Barrow Island and Shark Bay animals from a breeding facility at Dryandra. The reserve is closed, so no animals arrived later. The founders and animals born in the reserve, sampled each year from 2010 to 2018, were genotyped by RAD sequencing.
Format
A list with:
- genotypes
Integer matrix, 215 animals x 500 SNPs, counting Shark Bay (species 2) alleles (0, 1, 2;
NAmissing). The SNPs are a random 500 of the 1,233 that are fixed between the two founder groups, each on a separate RAD locus. They are not mapped.- groups
"ref1"(Barrow Island founders, 22),"ref2"(Shark Bay founders, 24) and"Matuwa2010"to"Matuwa2018"(animals born in the reserve, by year of first capture; 4 to 37 per year).- truth
Data frame, one row per group:
group,n,year,years_since_mixing,max_hybrid_age(an upper bound) andgenerations_at_3yr.- animals
Data frame, one row per animal:
id,group,year_sampledandpublished_class(the NewHybrids class published by Rick et al. 2019, Table S6:"BWI","DRY","F1","F2","F1BWI","F1DRY", or founder).- description
A short description.
Source
Rick K (2019) SNP dataset and Capture-Mark-Recapture dataset used in the analysis for the paper Rick et al.: Population genomics of Bettongia lesueur: admixing increases genetic diversity with no evidence of outbreeding depression. Mendeley Data, version 1, doi:10.17632/vg983472v3.1 (file "SNP dataset of Bettongia lesueur at Matuwa from STACKS pipeline.vcf"). Licensed under CC BY 4.0; a subset of SNPs was taken and genotypes recoded (see data-raw/bettongs.R).
Truth
Mixing started in 2010. Bettongs can breed in their first year, so an
animal first caught in year Y is at most Y - 2010 generations from the
pure founders (max_hybrid_age); this upper bound is the only firm fact.
With the average generation length of three years, the expected age is
about (Y - 2010) / 3 (generations_at_3yr). Pure animals of both sources
kept breeding inside the fence, so new F1s and first backcrosses appear
every year, and most hybrids are much younger than the bound. Year is the
year of first capture, not of birth.
About a quarter of heterozygotes are called homozygous (F1s show H of
about 0.75 instead of 1), so use het_dropout = 0.25 in
classify_hybrids(). The published classes are model-based, not known
pedigrees; a few disagree with the genotypes (D6056 and D6057 are listed
as F1 but are pure Barrow Island; D5893 is listed as Barrow Island but
has a hybrid index of 0.38).
Licence
The genotypes are from Mendeley Data and were released under CC BY 4.0, which requires attribution: cite Rick et al. (2019) and the dataset (see Source). The founder source and sampling year of each animal, and the published classes, come from Table S6 of Rick et al. (2019), an open access article under CC BY 4.0. Changes made: 500 SNPs were selected, genotypes were recoded to count Shark Bay alleles, and only the animal labels listed above were kept. No locality data are included.
References
Rick K, Ottewell K, Lohr C, Thavornkanlapachai R, Byrne M, Kennington WJ (2019) Population genomics of Bettongia lesueur: admixing increases genetic diversity with no evidence of outbreeding depression. Genes 10:851. doi:10.3390/genes10110851
Examples
mk <- diagnostic_markers(bettongs$genotypes, bettongs$groups, "ref1", "ref2")
sc <- hybrid_scores(bettongs$genotypes, mk)
cl <- classify_hybrids(sc, het_dropout = 0.25)
table(bettongs$groups, cl$class)
#>
#> BC1_species1 BC1_species2 BC2_species1 F1 F2 later pure1 pure2
#> Matuwa2010 0 0 0 0 0 0 4 0
#> Matuwa2011 0 0 0 2 0 1 9 3
#> Matuwa2012 0 1 0 7 0 3 5 3
#> Matuwa2013 2 1 0 7 1 10 9 7
#> Matuwa2014 5 1 1 4 1 14 6 1
#> Matuwa2015 1 1 1 3 1 7 2 0
#> Matuwa2016 0 0 0 1 0 12 2 0
#> Matuwa2017 4 1 0 1 0 5 4 0
#> Matuwa2018 3 0 2 1 1 6 2 0
#> ref1 0 0 0 0 0 0 22 0
#> ref2 0 0 0 0 0 0 0 24