Estimating admixture pedigrees of recent hybrids without a contiguous reference genome
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Estimating admixture pedigrees of recent hybrids without a contiguous reference genome. / Garcia-Erill, Genís; Hanghøj, Kristian; Heller, Rasmus; Wiuf, Carsten; Albrechtsen, Anders.
In: Molecular Ecology Resources, Vol. 23, No. 7, 2023, p. 1604-1619.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - Estimating admixture pedigrees of recent hybrids without a contiguous reference genome
AU - Garcia-Erill, Genís
AU - Hanghøj, Kristian
AU - Heller, Rasmus
AU - Wiuf, Carsten
AU - Albrechtsen, Anders
N1 - Publisher Copyright: © 2023 John Wiley & Sons Ltd.
PY - 2023
Y1 - 2023
N2 - The genome of recently admixed individuals or hybrids has characteristic genetic patterns that can be used to learn about their recent admixture history. One of these are patterns of interancestry heterozygosity, which can be inferred from SNP data from either called genotypes or genotype likelihoods, without the need for information on genomic location. This makes them applicable to a wide range of data that are often used in evolutionary and conservation genomic studies, such as low-depth sequencing mapped to scaffolds and reduced representation sequencing. Here we implement maximum likelihood estimation of interancestry heterozygosity patterns using two complementary models. We furthermore develop apoh (Admixture Pedigrees of Hybrids), a software that uses estimates of paired ancestry proportions to detect recently admixed individuals or hybrids, and to suggest possible admixture pedigrees. It furthermore calculates several hybrid indices that make it easier to identify and rank possible admixture pedigrees that could give rise to the estimated patterns. We implemented apoh both as a command line tool and as a Graphical User Interface that allows the user to automatically and interactively explore, rank and visualize compatible recent admixture pedigrees, and calculate the different summary indices. We validate the performance of the method using admixed family trios from the 1000 Genomes Project. In addition, we show its applicability on identifying recent hybrids from RAD-seq data of Grant's gazelle (Nanger granti and Nanger petersii) and whole genome low-depth data of waterbuck (Kobus ellipsiprymnus) which shows complex admixture of up to four populations.
AB - The genome of recently admixed individuals or hybrids has characteristic genetic patterns that can be used to learn about their recent admixture history. One of these are patterns of interancestry heterozygosity, which can be inferred from SNP data from either called genotypes or genotype likelihoods, without the need for information on genomic location. This makes them applicable to a wide range of data that are often used in evolutionary and conservation genomic studies, such as low-depth sequencing mapped to scaffolds and reduced representation sequencing. Here we implement maximum likelihood estimation of interancestry heterozygosity patterns using two complementary models. We furthermore develop apoh (Admixture Pedigrees of Hybrids), a software that uses estimates of paired ancestry proportions to detect recently admixed individuals or hybrids, and to suggest possible admixture pedigrees. It furthermore calculates several hybrid indices that make it easier to identify and rank possible admixture pedigrees that could give rise to the estimated patterns. We implemented apoh both as a command line tool and as a Graphical User Interface that allows the user to automatically and interactively explore, rank and visualize compatible recent admixture pedigrees, and calculate the different summary indices. We validate the performance of the method using admixed family trios from the 1000 Genomes Project. In addition, we show its applicability on identifying recent hybrids from RAD-seq data of Grant's gazelle (Nanger granti and Nanger petersii) and whole genome low-depth data of waterbuck (Kobus ellipsiprymnus) which shows complex admixture of up to four populations.
KW - admixture
KW - genomics
KW - Hybridization
KW - lowdepth sequencing
KW - non-model organisms
KW - RADseq
U2 - 10.1111/1755-0998.13830
DO - 10.1111/1755-0998.13830
M3 - Journal article
C2 - 37400991
AN - SCOPUS:85164317697
VL - 23
SP - 1604
EP - 1619
JO - Molecular Ecology
JF - Molecular Ecology
SN - 0962-1083
IS - 7
ER -
ID: 359651431