Table 1.

Supergenes Identified Using Genomic Methods, Including Information on the Trait under Selection, the Type of Selection Maintaining Polymorphism, the Inferred Age, Size, Gene Content, Identification Strategy, and Evolutionary Genetic Evidence for Degeneration

Trait (Locus)	Lineage	Origin	Structural Variation	Selection	Age (Myr)	Size (kb)	No. Genes in Region	Candidate Genes	ID Strategy	Signs of Degeneration	Refs
Batesian mimicry wing color patterning (H locus)	Papilio 1. polytes 2. memnon	Multiple	1. Inversion	Positive frequency-dependent selection	Unknown	1. 130 2. 168	3	doublesex, Nach-like, and UXT	1. Genetic association mapping, morph-specific expression 2. Coverage, genetic differentiation	Accumulation of TEs and repetitive sequences	Clarke and Sheppard (1960); Kunte et al. (2014); Nishikawa et al. (2015); Komata et al. (2016); Iijima et al. (2018)
Batesian mimicry wing color patterning (P locus)	Heliconius numata	Single	Inversion introduced by introgression	Antagonistic frequency-dependent selection	Inversion: 2.41, introgression: 2.30–2.24	P1 = 400 P2 = 200 P3 = 1,150	P1 = 21 P2 = 15 P3 = 71	cortex	Genetic linkage mapping, linkage disequilibrium (LD) analyses in natural populations and positional cloning	Accumulation of deleterious mutations and TEs, degenerative expansion	Joron et al. (2006, 2011); Chouteau et al. (2017); Jay et al. (2018, 2021); Saenko et al. (2019)
Colony social organization (Social S-locus)	Formica	Single	Inversion	Maternal effect killer in F. selysii	40–20	11,000	Varies	Knockout, serine–threonine kinase STK32B, MRPL34, RPUSD4 and G9A	Genetic association mapping, genetic differentiation between haplotypes, morphotype–genotype association	No major evidence for degeneration, low differentiation between haplotypes except at clusters of trans-species SNPs	Purcell et al. (2014); Avril et al. (2020); Brelsford et al. (2020)
Colony social organization (Social S-locus)	Solenopsis	Single	Two large inversions	SB/SB queens killed in polygyne colonies	0.5	13,000	616	Gp-9	Genetic association mapping, differential expression analyses	High frequency of deleterious mutations, repetitive elements, degenerative expansion	Wang et al. (2013); Stolle et al. (2019); Yan et al. (2020); Arsenault et al. (2020)
Cryptic coloration morphs (Mel-Stripe locus; m, U, and S variants)	Timema	Single	Inversion	Balancing selection, spatial heterogeneity	Between m and U :13.5–8.0; between U and S: 2.7–1.8	13,000	83	A 1,000-kb deletion in this region controls coloration across several species	Genome-wide association study (GWAS), differences in read depth coverage	Not studied	Nosil et al. (2018); Villoutreix et al. (2020)
Heterostyly (S-locus)	Primula	Single	Insertion	Disassortative mating, long-term balancing selection	50	278	5	CYP734A50 (style length), GLOT/GLO2 (anther position), KFB, PUM, and CCM	Differentially expressed genes in specific floral organs of the two floral morphs, identification of S-linked loci, genetic and physical maps, comparison of S haplotype sequences, functional studies of both CYP734A50 and GLOT/GLO2	TEs accumulation: 64% in region versus 37% genome wide	Huu et al. (2016, 2020); Li et al. (2016); Burrows and McCubbin (2017); Cocker et al. (2018)
Heterostyly (S-locus)	Turnera	Single	Three hemizygous genes + two inversions	Disassortative mating, long-term balancing selection	Unknown	241	21 + 3	TsBAHD (pistils), TsSPH1 and TsYUC6 (stamens)	Deletion mapping to sequence BAC clones and genome scaffolds to construct haplotypes, organ-specific gene expression	Higher TE content in dominant S-haplotype than in recessive s-haplotype, two inversions (unclear if cause or consequence of suppressed recombination)	Shore et al. (2019)
Male mating morphs	Philomachus pugnax	Single	Inversion	Balancing selection	3.8	4,400	25	HSD17B2, SDR42E1, ZDHHC7, and CYB5B (all involved in steroid metabolism)	Genetic linkage mapping, GWAS, genetic sequence divergence analyses	Not studied	Küpper et al. (2016); Lamichhaney et al. (2016)
Male-restricted dimorphism (api locus)	Acyrthosiphon pisum species complex	Single	Insertion	Balancing selection	10	120	12	follistatin	QTL analysis, coverage differences and genetic sequence differentiation between morphs	Not studied	Li et al. (2020)
Mating morphs (ZAL2/ZAL2m)	Zonotrichia albicollis	Single	Two inversions	Disassortative mating	2.5–1.9	100,000	1,137	ESR1 (aggressiveness) and VIP (aggressiveness, parental behavior), FIG4 and LYST (pigmentation)	Comparative chromosome painting, cytogenetic mapping, genetic sequence diversity and divergence analyses, LD analyses in natural populations	Reduced genetic diversity, excess of nonsynonymous mutations, no substantial degeneration but gene expression changes	Thomas et al. (2008); Tuttle et al. (2016); Sun et al. (2018); Maney et al. (2020); Horton et al. (2020); Merritt et al. (2020)
Mating type (MAT loci)	Microbotryum	Multiple	Chromosomal rearrangements, fusion of the MAT chromosomes	Balancing selection	Five independent times in the last 2.3–0.2	1,000–10,000	120–547	Homeodomain transcription factor genes PD and HD loci, responsible for pre- and postfertilization compatibility	Cosegregation of MAT type, chromosome dimorphism and markers; finding of contigs carrying PR and HD, comparative genomics (homology and synteny)	Gene losses, TEs accumulation	Branco et al. (2017, 2018)
Rainbow trout migration	Oncorhynchus mykiss	Single	Two inversions	Sexually antagonistic balancing selection	1.5	5,500	1,091	DMRTA2, AMH, NR5A2, RORC1, RXRA, LEPR, CENPR, CLOCK, PDCL, PPEF2, RX3, and MAPK10 (JNK3)	Genetic linkage mapping, genetic sequence diversity, and divergence analyses	Not studied	Pearse et al. (2019)
Sperm morphology	Taeniopygia guttata	Single	Z-linked inversion	Heterozygote advantage	Unknown	∼63,000	648	GADD45G, LRRC2, C9orf3, FBXL17, DMRT2, LINGO2, ZNF462, and RAD23B	GWAS, trait artificial selection, population genetic differentiation, expression quantitative trait locus analysis	Not studied	Kim et al. (2017)