Dataset.

### Appendix S1 "Probabilistic genetic identification of wild boar hybridization to support control of invasive wild pigs (Sus scrofa)"

Digital.CSIC. Repositorio Institucional del CSIC

oai:digital.csic.es:10261/362386

##### Digital.CSIC. Repositorio Institucional del CSIC

- Smyser, Timothy J.
- Pfaffelhuber, Peter
- Giglio, Rachael M.
- DeSaix, Matthew G.
- Davis, Amy J.
- Bowden, Courtney F.
- Tabak, Michael A.
- Manunza, Arianna
- Bâlteanu, Valentin Adrian
- Amills, Marcel
- Iacolina, Laura
- Walker, Pamela
- Lessard, Carl
- Piaggio, Antoinette J.

Figure S1. Flow chart illustrating the workflow for characterizing the probability that a given Sus scrofa high density single nucleotide polymorphism (SNP) genotype could be described under the null hypothesis – descending strictly from contributions from domestic pigs – relative to the alternative hypothesis of allowing for European wild boar ancestry. Table S1. A complete list of the high-density single nucleotide polymorphism (SNP) Sus scrofa genotypes included in the study, with 1,421 reference samples organized into five groups
(mixed-commercial breeds, Durocs, heritage breeds, primitive breeds, and European wild boar) for the development of the Delta Likelihood test static, and, for evaluation of the Delta Likelihood approach, a test set of 435 genotypes from 29 additional domestic breeds and 6,566 wild pigs sampled across the invaded range within the contiguous United States. The original publishing source for genotypes is presented in the table with complete references below. Figure S2. Illustration of the genetic structure, as revealed with principal component analysis (plotting principal component 1 versus 2), among the five reference groups of Sus scrofa genotyped with a high-density single nucleotide polymorphism (SNP) array for the development of the Delta Likelihood statistic – an approach to probabilistically describe that a given genotype possesses wild boar ancestry in full or in part (i.e., a wild boar-domestic pig hybrid). Figure S3. Barplots illustrating genetic structure among the 1,421 genotypes that comprise five reference groups of Sus scrofa – organized as mixed-commercial breeds of domestic pig, Durocs, heritage breeds, primitive breeds, and European wild boar – as revealed with high-density single nucleotide polymorphism (SNP) genotypes and leave-one-out analyses conducted in ADMIXTURE (v1.3.0; Alexander et al., 2009) in a supervised framework as described in Smyser et al. (2020). Figure S4. Delta Likelihood statistics calculated from high-density single nucleotide polymorphism (SNP) genotypes for Sus scrofa reference genotypes, organized into reference groups representing mixed-commercial breeds (n = 310), Durocs (n = 159), heritage breeds (n =381), primitive breeds (n = 189), and European wild boar (n = 382); plots represent kernel density estimates of Delta Likelihood statistics for the respective reference groups in which the loci retained for analysis were pruned for linkage disequilbrium (LD) base on the specific reference group listed in the plot title. Pruning for LD based on the heritage reference group resulted in the greatest difference between the upper tail of the kernel density estimate observed among the domestic pig reference groups versus the lower tail of the wild boar reference group (difference of 36.07 when LD pruning was based on the heritage reference group versus 32.72 for the mixed-commercial reference group, 28.79 for Duroc, 35.17 for primitive, and 30.79 for wild boar); thus, the set of 18,790 loci based on the heritage reference set LD prune was retained for subsequent analyses. Table S2. The statistical distribution and associated parameters for respective distributions fitted to Delta Likelihood statistics calculated for domestic pig reference groups (i.e., mixedcommercial breeds, Durocs, heritage breeds, primitive breeds) based on bootstrapped iterations in which the composition of the specific genotypes included in the reference groups were resampled with replacement 1,000 times. Figure S5. Kernel density estimates of Delta Likelihood statistics calculated with 18,790 single nucleotide polymorphic (SNP) loci for Sus scrofa reference genotypes, organized into reference groups representing mixed-commercial breeds (n = 310), Durocs (n = 159), heritage breeds (n = 381), primitive breeds (n = 189), European wild boar (n = 382) and an empirical test set of an additional 29 domestic breeds, represented by 435 genotypes, that were excluded from the reference set. Figure S6. Delta Likelihood statistics calculated from simulated high-density single nucleotide polymorphism (SNP) genotypes (18,790 loci) for Sus scrofa in which genotypes were simulated with R package gscramble (Anderson 2023, R Development Core Team 2023) from fourgeneration pedigrees established by randomly sampling without replacement a total of 16 genotypes from one of four domestic pig reference groups (16 – 1 genotypes drawn from either mixed-commercial, Duroc, heritage, or primitive reference groups) and a complementary number of genotypes (0 – 15) drawn from the wild boar reference group. Following four generations of one-to-one pairing with no inbreeding conducted within the simulation, while allowing for biologically realistic rates of recombination (1 centimorgan per megabase) to reflect the linkage structure among proximate loci and tracking the proportion of each genotype attributable to wild boar ancestry versus domestic pig ancestry, we randomly selected a single simulated genotype for analysis from the 64,000 iterations conducted., Peer reviewed

**DOI:**http://hdl.handle.net/10261/362386

Digital.CSIC. Repositorio Institucional del CSIC

oai:digital.csic.es:10261/362386

**HANDLE:**http://hdl.handle.net/10261/362386

Digital.CSIC. Repositorio Institucional del CSIC

oai:digital.csic.es:10261/362386

**Ver en:**http://hdl.handle.net/10261/362386

Digital.CSIC. Repositorio Institucional del CSIC

oai:digital.csic.es:10261/362386

No hay resultados en la búsqueda

No hay resultados en la búsqueda

×
#### 1 Versiones

#### 1 Versiones

Digital.CSIC. Repositorio Institucional del CSIC

oai:digital.csic.es:10261/362386

Dataset. 2024
#### APPENDIX S1 "PROBABILISTIC GENETIC IDENTIFICATION OF WILD BOAR HYBRIDIZATION TO SUPPORT CONTROL OF INVASIVE WILD PIGS (SUS SCROFA)"

##### Digital.CSIC. Repositorio Institucional del CSIC

- Smyser, Timothy J.
- Pfaffelhuber, Peter
- Giglio, Rachael M.
- DeSaix, Matthew G.
- Davis, Amy J.
- Bowden, Courtney F.
- Tabak, Michael A.
- Manunza, Arianna
- Bâlteanu, Valentin Adrian
- Amills, Marcel
- Iacolina, Laura
- Walker, Pamela
- Lessard, Carl
- Piaggio, Antoinette J.

Figure S1. Flow chart illustrating the workflow for characterizing the probability that a given Sus scrofa high density single nucleotide polymorphism (SNP) genotype could be described under the null hypothesis – descending strictly from contributions from domestic pigs – relative to the alternative hypothesis of allowing for European wild boar ancestry. Table S1. A complete list of the high-density single nucleotide polymorphism (SNP) Sus scrofa genotypes included in the study, with 1,421 reference samples organized into five groups
(mixed-commercial breeds, Durocs, heritage breeds, primitive breeds, and European wild boar) for the development of the Delta Likelihood test static, and, for evaluation of the Delta Likelihood approach, a test set of 435 genotypes from 29 additional domestic breeds and 6,566 wild pigs sampled across the invaded range within the contiguous United States. The original publishing source for genotypes is presented in the table with complete references below. Figure S2. Illustration of the genetic structure, as revealed with principal component analysis (plotting principal component 1 versus 2), among the five reference groups of Sus scrofa genotyped with a high-density single nucleotide polymorphism (SNP) array for the development of the Delta Likelihood statistic – an approach to probabilistically describe that a given genotype possesses wild boar ancestry in full or in part (i.e., a wild boar-domestic pig hybrid). Figure S3. Barplots illustrating genetic structure among the 1,421 genotypes that comprise five reference groups of Sus scrofa – organized as mixed-commercial breeds of domestic pig, Durocs, heritage breeds, primitive breeds, and European wild boar – as revealed with high-density single nucleotide polymorphism (SNP) genotypes and leave-one-out analyses conducted in ADMIXTURE (v1.3.0; Alexander et al., 2009) in a supervised framework as described in Smyser et al. (2020). Figure S4. Delta Likelihood statistics calculated from high-density single nucleotide polymorphism (SNP) genotypes for Sus scrofa reference genotypes, organized into reference groups representing mixed-commercial breeds (n = 310), Durocs (n = 159), heritage breeds (n =381), primitive breeds (n = 189), and European wild boar (n = 382); plots represent kernel density estimates of Delta Likelihood statistics for the respective reference groups in which the loci retained for analysis were pruned for linkage disequilbrium (LD) base on the specific reference group listed in the plot title. Pruning for LD based on the heritage reference group resulted in the greatest difference between the upper tail of the kernel density estimate observed among the domestic pig reference groups versus the lower tail of the wild boar reference group (difference of 36.07 when LD pruning was based on the heritage reference group versus 32.72 for the mixed-commercial reference group, 28.79 for Duroc, 35.17 for primitive, and 30.79 for wild boar); thus, the set of 18,790 loci based on the heritage reference set LD prune was retained for subsequent analyses. Table S2. The statistical distribution and associated parameters for respective distributions fitted to Delta Likelihood statistics calculated for domestic pig reference groups (i.e., mixedcommercial breeds, Durocs, heritage breeds, primitive breeds) based on bootstrapped iterations in which the composition of the specific genotypes included in the reference groups were resampled with replacement 1,000 times. Figure S5. Kernel density estimates of Delta Likelihood statistics calculated with 18,790 single nucleotide polymorphic (SNP) loci for Sus scrofa reference genotypes, organized into reference groups representing mixed-commercial breeds (n = 310), Durocs (n = 159), heritage breeds (n = 381), primitive breeds (n = 189), European wild boar (n = 382) and an empirical test set of an additional 29 domestic breeds, represented by 435 genotypes, that were excluded from the reference set. Figure S6. Delta Likelihood statistics calculated from simulated high-density single nucleotide polymorphism (SNP) genotypes (18,790 loci) for Sus scrofa in which genotypes were simulated with R package gscramble (Anderson 2023, R Development Core Team 2023) from fourgeneration pedigrees established by randomly sampling without replacement a total of 16 genotypes from one of four domestic pig reference groups (16 – 1 genotypes drawn from either mixed-commercial, Duroc, heritage, or primitive reference groups) and a complementary number of genotypes (0 – 15) drawn from the wild boar reference group. Following four generations of one-to-one pairing with no inbreeding conducted within the simulation, while allowing for biologically realistic rates of recombination (1 centimorgan per megabase) to reflect the linkage structure among proximate loci and tracking the proportion of each genotype attributable to wild boar ancestry versus domestic pig ancestry, we randomly selected a single simulated genotype for analysis from the 64,000 iterations conducted., Peer reviewed

There are no results for this search

1106