Table 1.
Summary of studies reviewed.
| Group | Donor | Recipient | Data | Method for detection of introgression | Method for detection of Selection | Adaptive trait | Publication |
|---|---|---|---|---|---|---|---|
| Animal | Anopheles gambiae | A. coluzzi | Genomic data | Diagnostic alleles | Haplotype based test; test for temporal evolution of allele frequencies | Pesticide resistance | Lynd et al., 2010 |
| Animal | Anopheles gambiae | A. coluzzi | Genomic data | Diagnostic alleles | Differentiation approach; diversity statistics | Pesticide resistance | Norris et al., 2015 |
| Animal | Drosophila yakuba | D. santomea | Genomic data (mtDNA) | Genes genealogy; isolation with migration model | Coalescent simulations | na | Llopart et al., 2014 |
| Animal | Mus spretus | M. m. domesticus | Genomic and phenotypic data | Genes genealogy; Hudson–Kreitman–Aguade test | Differentiation approach; fitness measures | Pesticide resistance | Song et al., 2011 |
| Animal | Mus spretus | M. m. domesticus | Genomic data | Genes genealogy | XP-CLR | Pesticide resistance | Liu et al., 2015 |
| Animal | Mus musculus musculus | M. m. domesticus | Genomic data | Local ancestry inference | XP-CLR; differentiation approach; coalescent simulations | Genetic disease, alpha-amylase genes | Staubach et al., 2012 |
| Animal | Oncorhynchus mykiss | O. clarkii lewisi | Genomic data | Diagnostic alleles | Heterogeneity test of Long (1991) | Fecundity | Hohenlohe et al., 2013 |
| Animal | Ambystoma tigrinum mavortium | A. californiense | Genomic data | Diagnostic alleles | Heterogeneity test of Long (1991) | na | Fitzpatrick et al., 2009 |
| Animal | Sus sp. | Sus scrofa domesticus | Genomic data | Genes genealogy | Differentiation approach | Highland adaptation | Ai et al., 2015 |
| Animal | Sus celebensis | Sus scrofa domesticus | Genomic data | Genes genealogy; differentiation statistics | Differentiation approach | Aggressive behavior | Zhu et al., 2017 |
| Animal | Canis lupus familiaris | C. lupus lupus | Genomic data | Genes genealogy | Haplotype based test | Concealment during predation | Anderson et al., 2009 |
| Animal | C. lupus lupus | C. l. familiaris | Genomic data | D statistic | Haplotype based test; differentiation outlier approach | Highland adaptation | Miao et al., 2016 |
| Animal | Ovis aries | Ovis aries | Genomic data | Local ancestry inference; populations genealogy | Differentiation outlier approach | na | Rochus et al., 2018 |
| Animal | Anguilla rostrata | A. anguilla | Genomic data | Local ancestry inference | Differentiation outlier approach; allele frequencies outlier test | na | Gagnaire et al., 2009 |
| Animal | Heliconius melpomene | H. cydno clade | Genomic data | Genes genealogy; isolation with migration model, linkage disequilibrium analysis | Not addressed, but trait previously tested as under natural selection | Wing pattern | Pardo-Diaz et al., 2012 |
| Animal | Heliconius melpomene | H. beskei | Genomic data | Gene genealogy; D-statistic and f-statistics | Not addressed, but trait previously tested as under natural selection | Wing pattern | Zhang et al., 2014 |
| Animal | Heliconius melpomene | H. cydno clade | Genomic data | Gene genealogy; D-statistic and f-statistics | Not addressed, but trait previously tested as under natural selection | Wing pattern | Enciso-Romero et al., 2017 |
| Animal | Lepus californicus | L. americanus | Genomic and phenotypic data | Phylogenetic analysis; differentiation statistics; f-statistics; coalescent simulations | Composite likelihood ratio (CLR) test; estimation of selection coefficient | Winter-brown-color coat | Jones et al., 2018 |
| Human | Homo s. denisovans | H. s. sapiens | Genomic data | D statistic, S∗ statistic | Differentiation outlier approach | Highland adaptation | Huerta-Sánchez et al., 2014 |
| Human | Homo s. neanderthalensis, H. s. denisovans | H. s. sapiens | Genomic and expression data | Diagnostic alleles | McDonald–Kreitman test; haplotype based test; differentiation outlier approach | Immune response | Deschamps et al., 2016 |
| Human | Homo neanderthalensis, H. s. denisovans | H. s. sapiens | Genomic and expression data | Differentiation comparisons; haplotype length vs. ILS (incomplete lineage sorting) | Differentiation outlier approach; gene expression; genotype–phenotype association | Immune response | Dannemann et al., 2016 |
| Human | Homo neanderthalensis, H. s. denisovans | H. s. sapiens | Genomic data | F statistics, S∗ statistic | Coalescent simulations | Immune response and metabolism | Vernot et al., 2016 |
| Human | Homo neanderthalensis, H. s. denisovans | H. s. sapiens | Genomic data | Diagnostic alleles | Coalescent simulations | Immune response, defense, regulatory regions, pigmentation | Gittelman et al., 2016 |
| Human | Homo neanderthalensis, H. s. denisovans | H. s. sapiens | Genomic data | f statistics, diagnostic alleles, local ancestry inference | Differentiation outlier approach | Cold tolerance | Racimo et al., 2017 |
| Human | Homo s. neanderthalensis | H. s. sapiens | Genomic data | Genes genealogy | Allele frequencies outlier test | Immune response | Mendez et al., 2012 |
| Human | Homo s. neanderthalensis | H. s. sapiens | Genomic data | Diagnostic alleles | Coalescent simulations; haplotype based test | Immune response | Sams et al., 2016 |
| Human | Homo s. neanderthalensis | H. s. sapiens | Genomic data | Diagnostic alleles | Differentiation outlier approach; haplotype based test; XP-CLR; coalescent simulations | Immune response | Quach et al., 2016 |
| Human | H. s. sapiens | H. s. sapiens | Genomic data | Population genealogy; D statistic and f statistics | Allele frequencies outlier test | Highland adaptation | Jeong et al., 2014 |
| Plant | Arabidopsis lyrata | A. arenosa | Genomic data | f statistics | Differentiation outlier approach | Serpentine syndrome | Arnold et al., 2016 |
| Plant | Helianthus debilis | H. annuus | Phenotypic data | Experimental hybrid populations | Common garden experiments – Fitness measures | Herbivory, drought | Whitney et al., 2006, 2010 |
| Plant | Helianthus debilis | H. annuus | Genomic and phenotypic data | Experimental hybrid populations | Genotype–phenotype association – Fitness measures | Number of seeds and pollen export | Whitney et al., 2015 |
| Plant | Iris fulva | I. brevicaulis | Genomic and phenotypic data | Experimental hybrid populations | Genotype–phenotype association – Fitness measures | Flood tolerance | Martin et al., 2006 |
| Plant | Populus balsamifera | P. trichocarpa | Genomic, expression and phenotypic data | Local ancestry inference | Diversity statistics; genotype–phenotype association | Light response | Suarez-Gonzalez et al., 2016 |
| Plant | Populus balsamifera | P. trichocarpa | Genomic, expression and phenotypic data | Local ancestry inference | Diversity statistics | Disease resistance | Suarez-Gonzalez et al., 2018a |
| Plant | Zea mays mexicana | Z. m. mays | Genomic data | Local ancestry inference | Genotype–environment association | Highland adaptation | Hufford et al., 2013 |
| Plant | Oryza sativa japonica | Oryza sativa indica | Genomic data | Diagnostic alleles | Haplotype based test | Fragrance | Kovach et al., 2009 |
| Plant | Senecio squalidus | S. vulgaris | Genomic data | Diagnostic alleles | Not addressed but high related fitness trait | Flower asymmetry | Kim et al., 2008 |
| Plant | Arabidopsis halleri | A. lyrata | Genomic data | Differentiation comparisons; isolation with migration model | Not addressed but high related fitness trait | Pistil self-incompatibility | Castric et al., 2008 |
| Plant | Solanum microdontum or other wild species | S. tuberosum | Genomic data | Genes genealogy | Not addressed, but trait previously tested as under natural selection | Long-day-maturity phenotype | Hardigan et al., 2017 |
Species names for donor and recipient taxa are listed, as well as the type of data and methods used for (1) detection of the introgression and (2) detection of the selection. “Genomic data” term include s whole-genome sequences or candidates genes sequencing. “Genetic data refers to molecular markers such as QTL or SSR.”