LITERATURE CITED
Ascencio D, Diss G, Gagnon-Arsenault I, Dubé AK, DeLuna A, Landry CR.
2021. Expression attenuation as a mechanism of robustness against gene
duplication. Proceedings of the National Academy of Sciences of
the United States of America 118: 1-10.
Bachmann JA, Tedder A, Laenen B, Fracassetti M, Désamoré A,
Lafon-Placette C, Steige KA, Callot C, Marande W, Neuffer B, et
al. 2019. Genetic basis and timing of a major mating system shift inCapsella . New Phytologist 224: 505–517.
Barmentlo SH, Meirmans PG, Luijten SH, Triest L, Oostermeijer JGB. 2017.
Outbreeding depression and breeding system evolution in small, remnant
populations of Primula vulgaris : consequences for genetic rescue.Conservation Genetics 19: 545–554.
Barrett SCH. 2019. ‘A most complex marriage arrangement’: Recent
advances on heterostyly and unresolved questions. New Phytologist224: 1051–1067.
Bateson W, Gregory RP. 1905. On the inheritance of heterostylism inPrimula . Proceedings of the Royal Society of London. Series
B 76: 581–586.
Belaoussoff S, Shore JS. 1995. Floral correlates and fitness
consequences of mating-system variation in Turnera ulmifolia .Evolution 49: 545–556.
Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: A flexible trimmer for
Illumina sequence data. Bioinformatics 30: 2114–2120.
Busch JW, Joly S, Schoen DJ. 2011. Demographic signatures accompanying
the evolution of selfing in Leavenworthia alabamica .Molecular Biology and Evolution 28: 1717–1729.
Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K,
Madden TL. 2009. BLAST+: Architecture and applications. BMC
Bioinformatics 10: 1–9.
Charlesworth D. 2022. Primrose homostyles: A classic case of possible
balancing selection revisited. Molecular Ecology 32: 1–3.
Charlesworth B, Charlesworth D. 1979. The maintenance and breakdown of
distyly. The American Naturalist 114: 499–513.
Charlesworth B, Charlesworth D. 2000. The degeneration of Y chromosomes.Philosophical Transactions of the Royal Society B: Biological
Sciences 355: 1563–1572.
Charlesworth D, Morgan MT, Charlesworth B. 1990. Inbreeding depression,
genetic load, and the evolution of outcrossing rates in a multilocus
system with no linkage. Evolution 44: 1469-1489.
Cocker JM, Wright J, Li J, Swarbreck D, Dyer S, Caccamo M, Gilmartin PM.
2018. Primula vulgaris (primrose) genome assembly, annotation and
gene expression, with comparative genomics on the heterostyly supergene.Scientific Reports 8: 1-13.
Costa J, Torices R, Barrett SCH. 2019. Evolutionary history of the
buildup and breakdown of the heterostylous syndrome in Plumbaginaceae.New Phytologist 224: 1278– 1289.
Crosby JL. 1940. High proportions of homostyle plants in populations ofPrimula vulgaris . Nature 145: 672–673.
Crosby JL. 1949. Selection of an unfavourable gene-complex.Evolution 3: 212–230.
Curtis J, Curtis CF. 1985. Homostyle primroses re-visited. I. Variation
in time and space. Heredity 54: 227–234.
Cutter AD. 2019. Reproductive transitions in plants and animals: selfing
syndrome, sexual selection and speciation. New Phytologist 224:
1080–1094.
Fisher R. 1941. Average excess and average effect of a gene
substitution. Annals of Eugenics 11: 53–63.
Ganders FR. 1979. The biology of heterostyly. New Zealand Journal
of Botany 17: 607–635.
Gao C, Zhou G, Ma C, Zhai W, Zhang T, Liu Z, Yang Y, Wu M, Yue Y, Duan
Z, et al. 2016. Helitron-like transposons contributed to the
mating system transition from out-crossing to self-fertilizing in
polyploid Brassica napus L. Scientific Reports 6: 1–10.
Garafutdinov RR, Galimova AA, Sakhabutdinova AR, Chemeris A V. 2016.
PCR-based evaluation of sequence specificity of DNA fragmentation by
ultrasound. Molecular Biology 50: 236–241.
Goldberg EE, Igic B. 2012. Tempo and mode in plant breeding system
evolution. Evolution 66: 3701–3709.
Gossmann TI, Woolfit M, Eyre-Walker A. 2011. Quantifying the variation
in the effective population size within a genome. Genetics 189:
1389–1402.
Gutiérrez-Valencia J, Fracassetti M, Berdan EL, Bunikis I, Soler L,
Dainat J, Kutschera VE, Losvik A, Désamoré A, Hughes PW, et al.2022. Genomic analyses of the Linum distyly supergene reveal
convergent evolution at the molecular level. Current Biology 32:
4360-4371.e6.
Gutiérrez-Valencia J, Hughes PW, Berdan EL, Slotte T. 2021. The genomic
architecture and evolutionary fates of supergenes. Genome Biology
and Evolution 13: 1–19.
Husband BC, Barrett SCH. 1993. Multiple origins of self-fertilization in
tristylous Eichhornia paniculata (Pontederiaceae): Inferences
from style morph and isozyme variation. Journal of Evolutionary
Biology 6: 591–608.
Huu CN, Kappel C, Keller B, Sicard A, Takebayashi Y, Breuninger H, Nowak
MD, Bäurle I, Himmelbach A, Burkart M, et al. 2016. Presence
versus absence of CYP734A50 underlies the style-length dimorphism
in primroses. eLife 5: 1–15.
Huu CN, Keller B, Conti E, Kappel C, Lenhard M. 2020. Supergene
evolution via stepwise duplications and neofunctionalization of a
floral-organ identity gene. Proceedings of the National Academy of
Sciences of the United States of America 117: 23148–23157.
Huu CN, Plaschil S, Himmelbach A, Kappel C, Lenhard M. 2022. Female
self-incompatibility type in heterostylous Primula is determined
by the brassinosteroid-inactivating cytochrome P450 CYP734A50 .Current Biology 32: 671-676.
Jacquemyn H, Endels P, Brys R, Hermy M, Woodell SRJ. 2009. Biological
flora of the British Isles: Primula vulgaris Huds. (P.
acaulis (L.) Hill). Journal of Ecology 97: 812–833.
Jennings LJ, Arcila ME, Corless C, Kamel-Reid S, Lubin IM, Pfeifer J,
Temple-Smolkin RL, Voelkerding K V., Nikiforova MN. 2017. Guidelines for
validation of next-generation sequencing–based oncology panels: a joint
consensus recommendation of the Association for Molecular Pathology and
College of American Pathologists. Journal of Molecular
Diagnostics 19: 341–365.
Keller B, Thomson JD, Conti E. 2014. Heterostyly promotes disassortative
pollination and reduces sexual interference in Darwin’s primroses:
Evidence from experimental studies. Functional Ecology 28:
1413–1425.
Kissling J, Barrett SCHH. 2013. Variation and evolution of herkogamy inExochaenium (Gentianaceae): Implications for the evolution of
distyly. Annals of Botany 112: 95–102.
Korunes KL, Samuk K. 2021. pixy: Unbiased estimation of nucleotide
diversity and divergence in the presence of missing data.Molecular Ecology Resources 21: 1359–1368.
Kumar S, Stecher G, Li M, Knyaz C, Tamura K. 2018. MEGA X: Molecular
evolutionary genetics analysis across computing platforms.Molecular Biology and Evolution 35: 1547–1549.
Kurian V, Richards AJ. 1997. A new recombinant in the heteromorphy “S”
supergene in Primula . Heredity 78: 383–390.
Lande R, Schemske DW. 1985. The evolution of self-fertilization and
inbreeding depression in plants. I. Genetic Models. Evolution 39:
24–40.
Lewis D, Jones DA. 1992. The genetics of heterostyly. In: Barrett S, ed.
The Evolution and Function of Heterostyly. Berlin: Springer-Verlag,
129–151.
Li J, Cocker JM, Wright J, Webster MA, McMullan M, Dyer S, Swarbreck D,
Caccamo M, Van Oosterhout C, Gilmartin PM. 2016. Genetic architecture
and evolution of the S-locus supergene in Primula vulgaris .Nature Plants 2: 1–7.
Li Z, Defoort J, Tasdighian S, Maere S, Van De Peer Y, De Smet R. 2015.
Gene duplicability of core genes is highly consistent across all
angiosperms. Plant Cell 28: 326-344.
Li H, Durbin R. 2009. Fast and accurate short read alignment with
Burrows-Wheeler transform. Bioinformatics 25: 1754–1760.
Lloyd DG, Webb CJ. 1992. The selection of heterostyly. In: Barrett S,
ed. The Evolution and Function of Heterostyly. Heidelberg:
Springer-Verlag Berlin, 179–207.
Mable BK, Hagmann J, Kim ST, Adam A, Kilbride E, Weigel D, Stift M.
2017. What causes mating system shifts in plants? Arabidopsis
lyrata as a case study. Heredity 118: 52–63.
Mather K, Winton D DE. 1941. Adaptation and counter-adaptation of the
breeding system in Primula . Annals of Botany 5: 297–311.
Matsui K, Yasui Y. 2020. Genetic and genomic research for the
development of an efficient breeding system in heterostylous
self-incompatible common buckwheat (Fagopyrum esculentum ).Theoretical and Applied Genetics 133: 1641–1653.
McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A,
Garimella K, Altshuler D, Gabriel S, Daly M, et al. 2010. The
Genome Analysis Toolkit: A MapReduce framework for analyzing
next-generation DNA sequencing data. Genome Research : 1297–1303.
McLeay RC, Bailey TL. 2010. Motif Enrichment Analysis: A unified
framework and an evaluation on ChIP data. BMC Bioinformatics 11:
1-11.
Mora-Carrera E, Stubbs RL, Keller B, Léveillé-Bourret É, de Vos JM,
Szövényi P, Conti E. 2021. Different molecular changes underlie the same
phenotypic transition: Origins and consequences of independent shifts to
homostyly within species. Molecular Ecology 32: 1–18.
Naiki A. 2012. Heterostyly and the possibility of its breakdown by
polyploidization. Plant Species Biology 27: 3–29.
Nasrallah JB. 2017. Plant mating systems: self-incompatibility and
evolutionary transitions to self-fertility in the mustard family.Current Opinion in Genetics and Development 47: 54–60.
Ness RW, Wright SI, Barrett SCH. 2010. Mating-system variation,
demographic history and patterns of nucleotide diversity in the
tristylous plant Eichhornia paniculata . Genetics 184:
381–392.
O’Malley RC, Huang SSC, Song L, Lewsey MG, Bartlett A, Nery JR, Galli M,
Gallavotti A, Ecker JR. 2016. Cistrome and epicistrome features shape
the regulatory DNA landscape. Cell 165: 1280–1292.
Ono K, Akagi T, Morimoto T, Wónsch A, Tao R. 2018. Genome re-sequencing
of diverse sweet cherry (Prunus avium ) individuals reveals a
modifier gene mutation conferring pollen-part self-compatibility.Plant and Cell Physiology 59: 1265–1275.
Poptsova MS, Il’Icheva IA, Nechipurenko DY, Panchenko LA, Khodikov M V.,
Oparina NY, Polozov R V., Nechipurenko YD, Grokhovsky SL. 2014.
Non-random DNA fragmentation in next-generation sequencing.Scientific Reports 4: 1–6.
Potente G, Léveillé-Bourret É, Yousefi N, Choudhury RR, Keller B, Diop
SI, Duijsings D, Pirovano W, Lenhard M, Szövényi P, et al. 2022.
Comparative genomics elucidates the origin of a supergene controlling
floral heteromorphism. Molecular Biology and Evolution 39: 1–16.
Quinlan AR, Hall IM. 2010. BEDTools: A flexible suite of utilities for
comparing genomic features. Bioinformatics 26: 841–842.
Rice A, McLysaght A. 2017. Dosage-sensitive genes in evolution and
disease. BMC Biology 15: 1-10.
Robinson JT, Thorvaldsdóttir H, Winckler W, Guttman M, Lander ES, Getz
G, Mesirov JP. 2011. Integrative genomics viewer. Nature
Biotechnology 29: 24–26.
Ruiz-Martín J, Santos-Gally R, Escudero M, Midgley JJ, Pérez-Barrales R,
Arroyo J. 2018. Style polymorphism in Linum (Linaceae): a case of
Mediterranean parallel evolution? Plant Biology 20: 100–111.
Schoen DJ., Johnston MO., L’Heureux A-M, Marsolais JV., Heureux A-ML’,
Marsolais JV. 1997. Evolutionary history of the mating system inAmsinckia (Boraginaceae). Evolution 51: 1090–1099.
Shimizu KK, Tsuchimatsu T. 2015. Evolution of selfing: Recurrent
patterns in molecular adaptation. Annual Review of Ecology,
Evolution, and Systematics 46: 593–622.
Shore JS, Hamam HJ, Chafe PDJ, Labonne JDJ, Henning PM, McCubbin AG.
2019. The long and short of the S-locus in Turnera(Passifloraceae). New Phytologist 224: 1316–1329.
Tsuchimatsu T, Kaiser P, Yew CL, Bachelier JB, Shimizu KK. 2012. Recent
loss of self-incompatibility by degradation of the male component in
allotetraploid Arabidopsis kamchatica . PLoS Genetics 8:
16–19.
Stebbins GL. 1957. Self fertilization and population variability in the
higher plants. The American Naturalist 91: 337–354.
Tasdighian S, Van Bel M, Li Z, Van De Peer Y, Carretero-Paulet L, Maere
S. 2017. Reciprocally retained genes in the angiosperm lineage show the
hallmarks of dosage balance sensitivity. Plant Cell 29:
2766-2785.
de Vos JM, Hughes CE, Schneeweiss GM, Moore BR, Conti E. 2014.
Heterostyly accelerates diversification via reduced extinction in
Darwin’s primroses. Proceedings of the Royal Society B: Biological
Sciences 281: 20140075.
Williamson RJ, Josephs EB, Platts AE, Hazzouri KM, Haudry A, Blanchette
M, Wright SI. 2014. Evidence for widespread positive and negative
selection in coding and conserved noncoding regions of Capsella
grandiflora . PLoS Genetics 10: 1-12.
Yu CP, Lin JJ, Li WH. 2016. Positional distribution of transcription
factor binding sites in Arabidopsis thaliana . Scientific
Reports 6: 1–7.
Yuan S, Barrett SCH, Duan T, Qian X, Shi M, Zhang D. 2017. Ecological
correlates and genetic consequences of evolutionary transitions from
distyly to homostyly. Annals of Botany 120: 775–789.
Yuan S, Barrett SCH, Li C, Li X, Xie K, Zhang D. 2018. Genetics of
distyly and homostyly in a self-compatible Primula .Heredity : 1–10.
Zhao Z, Zhang Y, Shi M, Liu Z, Xu Y, Luo Z, Yuan S, Tu T, Sun Z, Zhang
D, et al. 2023. Genomic evidence supports the genetic convergence
of a supergene controlling the distylous floral syndrome. New
Phytologist 237: 601–614.
Zhong L, Barrett SCH, Wang X, Wu Z, Sun H, Li D, Wang H, Zhou W. 2019.
Phylogenomic analysis reveals multiple evolutionary origins of selfing
from outcrossing in a lineage of heterostylous plants. New
Phytologist 224: 1290–1303.
Zhou W, Barrett SCH, Li HD, Wu ZK, Wang XJ, Wang H, Li DZ. 2017.
Phylogeographic insights on the evolutionary breakdown of heterostyly.New Phytologist 214: 1368–1380.
Zhou W, Barrett SCH, Wang H, Li DZ. 2012. Loss of floral polymorphism in
heterostylous Luculia pinceana (Rubiaceae): A molecular
phylogeographic perspective. Molecular Ecology 21: 4631–4645.