References
Abbott R. J. (1992). Plant invasions, interspecific hybridization and
the evolution of new plant taxa. Trends in ecology &
evolution , 7 (12), 401–405.
https://doi.org/10.1016/0169-5347(92)90020-C
Abbott, R., Albach, D., Ansell, S., Arntzen, J. W., Baird, S. J.,
Bierne, N., Boughman, J., Brelsford, A., Buerkle, C. A., Buggs, R.,
Butlin, R. K., Dieckmann, U., Eroukhmanoff, F., Grill, A., Cahan, S. H.,
Hermansen, J. S., Hewitt, G., Hudson, A. G., Jiggins, C., Jones, J.,
… Zinner, D. (2013). Hybridization and speciation. Journal
of evolutionary biology , 26 (2), 229–246.
https://doi.org/10.1111/j.1420-9101.2012.02599.x
Baack, E., Melo, M. C., Rieseberg, L. H., & Ortiz-Barrientos, D.
(2015). The origins of reproductive isolation in plants. The New
phytologist , 207 (4), 968–984.
https://doi.org/10.1111/nph.13424
Barker, M. S., Arrigo, N., Baniaga, A. E., Li, Z., & Levin, D. A.
(2016). On the relative abundance of autopolyploids and
allopolyploids. The New phytologist , 210 (2), 391–398.
https://doi.org/10.1111/nph.13698
Blanckaert, A., & Bank, C. (2018). In search of the Goldilocks zone for
hybrid speciation. PLoS genetics , 14 (9), e1007613.
https://doi.org/10.1371/journal.pgen.1007613
Blanckaert, A., Sriram, V., & Bank, C. (2023). In search of the
Goldilocks zone for hybrid speciation II: hard times for hybrid
speciation?. Evolution; international journal of organic
evolution , 77 (10), 2162–2172.
https://doi.org/10.1093/evolut/qpad125
Bock, D. G., Cai, Z., Elphinstone, C., González-Segovia, E.,
Hirabayashi, K., Huang, K., Keais, G. L., Kim, A., Owens, G. L., &
Rieseberg, L. H. (2023). Genomics of plant speciation. Plant
communications , 4 (5), 100599.
https://doi.org/10.1016/j.xplc.2023.100599
Brennan, A. C., Hiscock, S. J., & Abbott, R. J. (2019). Completing the
hybridization triangle: the inheritance of genetic incompatibilities
during homoploid hybrid speciation in ragworts
(Senecio ). AoB PLANTS , 11 (1), ply078.
https://doi.org/10.1093/aobpla/ply078
Buerkle, C. A., & Rieseberg, L. H. (2008). The rate of genome
stabilization in homoploid hybrid species. Evolution;
international journal of organic evolution , 62 (2), 266–275.
https://doi.org/10.1111/j.1558-5646.2007.00267.x
Buerkle, C. A., Morris, R. J., Asmussen, M. A., & Rieseberg, L. H.
(2000). The likelihood of homoploid hybrid
speciation. Heredity , 84 ( Pt 4) , 441–451.
https://doi.org/10.1046/j.1365-2540.2000.00680.x
Buerkle, C.A., Wolf, D.E., Rieseberg, L.H. (2003). The Origin and
Extinction of Species Through Hybridization. In: Brigham, C.A.,
Schwartz, M.W. (eds) Population Viability in Plants. Ecological
Studies , vol 165. Springer, Berlin, Heidelberg.
https://doi.org/10.1007/978-3-662-09389-4_5
Chapman, M. A., & Burke, J. M. (2007). Genetic divergence and hybrid
speciation. Evolution; international journal of organic
evolution , 61 (7), 1773–1780.
https://doi.org/10.1111/j.1558-5646.2007.00134.x
Comeault A. A. (2018). The genomic and ecological context of
hybridization affects the probability that symmetrical incompatibilities
drive hybrid speciation. Ecology and evolution , 8 (5),
2926–2937. https://doi.org/10.1002/ece3.3872
Cuevas, A., Ravinet, M., Saetre, G. P., & Eroukhmanoff, F. (2021).
Intraspecific genomic variation and local adaptation in a young hybrid
species. Molecular ecology , 30 (3), 791–809.
https://doi.org/10.1111/mec.15760
Dagilis, A. J., Peede, D., Coughlan, J. M., Jofre, G. I., D’Agostino, E.
R. R., Mavengere, H., Tate, A. D., & Matute, D. R. (2022). A need for
standardized reporting of introgression: Insights from studies across
eukaryotes. Evolution letters , 6 (5), 344–357.
https://doi.org/10.1002/evl3.294
Goulet-Scott, B. E., Garner, A. G., & Hopkins, R. (2021). Genomic
analyses overturn two long-standing homoploid hybrid speciation
hypotheses. Evolution; international journal of organic
evolution , 75 (7), 1699–1710.
https://doi.org/10.1111/evo.14279
Grant, V. (1981). Plant Speciation . New York Chichester, West
Sussex: Columbia University
Press. https://doi.org/10.7312/gran92318
Green, R. E., Krause, J., Briggs, A. W., Maricic, T., Stenzel, U.,
Kircher, M., Patterson, N., Li, H., Zhai, W., Fritz, M. H., Hansen, N.
F., Durand, E. Y., Malaspinas, A. S., Jensen, J. D., Marques-Bonet, T.,
Alkan, C., Prüfer, K., Meyer, M., Burbano, H. A., Good, J. M., …
Pääbo, S. (2010). A draft sequence of the Neandertal
genome. Science (New York, N.Y.) , 328 (5979), 710–722.
https://doi.org/10.1126/science.1188021
Hermansen, J. S., Haas, F., Trier, C. N., Bailey, R. I., Nederbragt, A.
J., Marzal, A., & Saetre, G. P. (2014). Hybrid speciation through
sorting of parental incompatibilities in Italian
sparrows. Molecular ecology , 23 (23), 5831–5842.
https://doi.org/10.1111/mec.12910
Hudson, R. R., Kreitman, M., & Aguadé, M. (1987). A test of neutral
molecular evolution based on nucleotide
data. Genetics , 116 (1), 153–159.
https://doi.org/10.1093/genetics/116.1.153
Lamichhaney, S., Han, F., Webster, M. T., Andersson, L., Grant, B. R.,
& Grant, P. R. (2018). Rapid hybrid speciation in Darwin’s
finches. Science (New York, N.Y.) , 359 (6372), 224–228.
https://doi.org/10.1126/science.aao4593
Leducq, J. B., Nielly-Thibault, L., Charron, G., Eberlein, C., Verta, J.
P., Samani, P., Sylvester, K., Hittinger, C. T., Bell, G., & Landry, C.
R. (2016). Speciation driven by hybridization and chromosomal plasticity
in a wild yeast. Nature microbiology , 1 , 15003.
https://doi.org/10.1038/nmicrobiol.2015.3
Li, M., Zheng, Z., Liu, J., Yang, Y., Ren, G., Ru, D., Zhang, S., Du,
X., Ma, T., Milne, R., & Liu, J. (2021). Evolutionary origin of a
tetraploid Allium species on the Qinghai-Tibet Plateau. Molecular
ecology , 30 (22), 5780–5795.
https://doi.org/10.1111/mec.16168
Liu, B., Abbott, R. J., Lu, Z., Tian, B., & Liu, J. (2014). Diploid
hybrid origin of Ostryopsis intermedia (Betulaceae) in the Qinghai-Tibet
Plateau triggered by Quaternary climate change. Molecular
ecology , 23 (12), 3013–3027.
https://doi.org/10.1111/mec.12783
Lukhtanov VA, Shapoval NA, Anokhin BA, Saifitdinova AF, Kuznetsova VG.
Homoploid hybrid speciation and genome evolution via chromosome sorting.
Proc Biol Sci. 2015 May 22;282(1807):20150157. doi:
10.1098/rspb.2015.0157. Mallet, 2007;
Masello, J. F., Quillfeldt, P., Sandoval-Castellanos, E., Alderman, R.,
Calderón, L., Cherel, Y., Cole, T. L., Cuthbert, R. J., Marin, M.,
Massaro, M., Navarro, J., Phillips, R. A., Ryan, P. G., Shepherd, L. D.,
Suazo, C. G., Weimerskirch, H., & Moodley, Y. (2019). Additive Traits
Lead to Feeding Advantage and Reproductive Isolation, Promoting
Homoploid Hybrid Speciation. Molecular biology and
evolution , 36 (8), 1671–1685.
https://doi.org/10.1093/molbev/msz090
Mavárez, J., Salazar, C. A., Bermingham, E., Salcedo, C., Jiggins, C.
D., & Linares, M. (2006). Speciation by hybridization in Heliconius
butterflies. Nature , 441 (7095), 868–871.
https://doi.org/10.1038/nature04738
Mayrose, I., Zhan, S. H., Rothfels, C. J., Magnuson-Ford, K., Barker, M.
S., Rieseberg, L. H., & Otto, S. P. (2011). Recently formed polyploid
plants diversify at lower rates. Science (New York,
N.Y.) , 333 (6047), 1257.
https://doi.org/10.1126/science.1207205
Meier, J. I., Marques, D. A., Mwaiko, S., Wagner, C. E., Excoffier, L.,
& Seehausen, O. (2017). Ancient hybridization fuels rapid cichlid fish
adaptive radiations. Nature communications , 8 , 14363.
https://doi.org/10.1038/ncomms14363
Monnet, F., Postel, Z., Touzet, P., Fraïsse, C., Van de Peer, Y.,
Vekemans, X., & Roux, C. (2023). Rapid establishment of species
barriers in plants compared to animals. bioRxivhttps://do.org/10.1101/2023.10.16.562535
Nevado, B., Harris, S. A., Beaumont, M. A., & Hiscock, S. J. (2020).
Rapid homoploid hybrid speciation in British gardens: The origin of
Oxford ragwort (Senecio squalidus). Molecular
ecology , 29 (21), 4221–4233.
https://doi.org/10.1111/mec.15630
Nieto Feliner, G., Álvarez, I., Fuertes-Aguilar, J., Heuertz, M.,
Marques, I., Moharrek, F., Piñeiro, R., Riina, R., Rosselló, J. A.,
Soltis, P. S., & Villa-Machío, I. (2017). Is homoploid hybrid
speciation that rare? An empiricist’s
view. Heredity , 118 (6), 513–516.
https://doi.org/10.1038/hdy.2017.7
Osborne, O. G., Batstone, T. E., Hiscock, S. J., & Filatov, D.
A. (2013). Rapid speciation with gene flow following the formation of
Mt. Etna. Genome Biology and
Evolution , 5 (9), 1704–1715. https://doi.org/10.1093/gbe/evt127
Ottenburghs J. (2018). Exploring the hybrid speciation continuum in
birds. Ecology and evolution , 8 (24), 13027–13034.
https://doi.org/10.1002/ece3.4558
Ottenburghs, J., Megens, H. J., Kraus, R. H. S., Madsen, O., van Hooft,
P., van Wieren, S. E., Crooijmans, R. P. M. A., Ydenberg, R. C.,
Groenen, M. A. M., & Prins, H. H. T. (2016). A tree of geese: A
phylogenomic perspective on the evolutionary history of True
Geese. Molecular phylogenetics and evolution , 101 ,
303–313. https://doi.org/10.1016/j.ympev.2016.05.021
Owens G. L. (2021). From common gardens to candidate genes: an elegant
case of homoploid hybrid speciation. Molecular
plant , 14 (2), 200–201.
https://doi.org/10.1016/j.molp.2020.11.020
Owens, G. L., Huang, K., Todesco, M., & Rieseberg, L. H. (2023).
Re-evaluating Homoploid Reticulate Evolution in Helianthus
Sunflowers. Molecular biology and evolution , 40 (2),
msad013. https://doi.org/10.1093/molbev/msad013
Papoli Yazdi, H., Ravinet, M., Rowe, M., Saetre, G. P., Guldvog, C. Ø.,
Eroukhmanoff, F., Marzal, A., Magallanes, S., & Runemark, A. (2022).
Extensive transgressive gene expression in testis but not ovary in the
homoploid hybrid Italian sparrow. Molecular
ecology , 31 (15), 4067–4077.
https://doi.org/10.1111/mec.16572
Ravinet, M., Elgvin, T. O., Trier, C., Aliabadian, M., Gavrilov, A., &
Sætre, G. P. (2018). Signatures of human-commensalism in the house
sparrow genome. Proceedings. Biological
sciences , 285 (1884), 20181246.
https://doi.org/10.1098/rspb.2018.1246
Rieseberg, L. H. (1997). Hybrid origins of plant species. Annual
Review of Ecology and Systematics 28 , 359-389.
https://doi.org/10.1146/annurev.ecolsys.28.1.359
Rieseberg, L. H., Raymond, O., Rosenthal, D. M., Lai, Z., Livingstone,
K., Nakazato, T., Durphy, J. L., Schwarzbach, A. E., Donovan, L. A., &
Lexer, C. (2003). Major ecological transitions in wild sunflowers
facilitated by hybridization. Science (New York,
N.Y.) , 301 (5637), 1211–1216.
https://doi.org/10.1126/science.1086949
Rokas, A., & Holland, P. W. (2000). Rare genomic changes as a tool for
phylogenetics. Trends in ecology & evolution, 15(11), 454–459.
https://doi.org/10.1016/s0169-5347(00)01967-4
Roux, C., Fraïsse, C., Romiguier, J., Anciaux, Y., Galtier, N., &
Bierne, N. (2016). Shedding Light on the Grey Zone of Speciation along a
Continuum of Genomic Divergence. PLoS biology , 14 (12),
e2000234. https://doi.org/10.1371/journal.pbio.2000234
Salazar, C., Baxter, S. W., Pardo-Diaz, C., Wu, G., Surridge, A.,
Linares, M., Bermingham, E., & Jiggins, C. D. (2010). Genetic evidence
for hybrid trait speciation in Heliconius butterflies. PLoS
genetics , 6 (4), e1000930.
https://doi.org/10.1371/journal.pgen.1000930
Schemske, D. W. (2000). Understanding the origin of species.Evolution; international journal of organic evolution , 54(3),
1069–1073, https://doi.org/10.1111/j.0014-3820.2000.tb00111.x
Schumer, M., Cui, R., Rosenthal, G. G., & Andolfatto, P. (2015).
Reproductive isolation of hybrid populations driven by genetic
incompatibilities. PLoS genetics , 11 (3), e1005041.
https://doi.org/10.1371/journal.pgen.1005041
Schumer, M., Rosenthal, G. G., & Andolfatto, P. (2014). How common is
homoploid hybrid speciation?. Evolution; international journal of
organic evolution , 68 (6), 1553–1560.
https://doi.org/10.1111/evo.12399
Schumer, M., Rosenthal, G. G., & Andolfatto, P. (2018). What do we mean
when we talk about hybrid speciation?. Heredity , 120 (4),
379–382. https://doi.org/10.1038/s41437-017-0036-z
Smith, S. A., & Donoghue, M. J. (2008). Rates of molecular evolution
are linked to life history in flowering plants. Science (New York,
N.Y.) , 322 (5898), 86–89.
https://doi.org/10.1126/science.1163197
Soltis, D. E., Buggs, R. J. A., Doyle, J. J., & Soltis, P. S. (2010).
What we still don’t know about polyploidy. Taxon 59 (5),
1387–1403. https://doi.org/10.1002/tax.595006
Stevison, L. S., Bailey, N. P., Szpiech, Z. A., Novak, T.
E., Melnick, D. J., Evans, B. J., & Wall, J. D. (2022). Evolution of
genes involved in the unusual genitals of the bear macaque, Macaca
arctoides . Ecology and Evolution , 12,
e8897. https://doi.org/10.1002/ece3.8897
Stull, G. W., Pham, K. K., Soltis, P. S., & Soltis, D. E. (2023). Deep
reticulation: the long legacy of hybridization in vascular plant
evolution. The Plant journal : for cell and molecular
biology , 114 (4), 743–766.
https://doi.org/10.1111/tpj.16142
Sun, Y., Lu, Z., Zhu, X., & Ma, H. (2020). Genomic basis of homoploid
hybrid speciation within chestnut trees. Nature
communications , 11 (1), 3375.
https://doi.org/10.1038/s41467-020-17111-w
Taylor, S. A., & Larson, E. L. (2019). Insights from genomes into the
evolutionary importance and prevalence of hybridization in
nature. Nature ecology & evolution , 3 (2), 170–177.
https://doi.org/10.1038/s41559-018-0777-y
Thompson, K. A., Brandvain, Y., Coughlan, J. M., Delmore, K. E., Justen,
H., Linnen, C. R., Ortiz-Barrientos, D., Rushworth, C. A., Schneemann,
H., Schumer, M., & Stelkens, R. (2023). The Ecology of Hybrid
Incompatibilities. Cold Spring Harbor perspectives in biology ,
a041440. Advance online publication.
https://doi.org/10.1101/cshperspect.a041440
Wang, D., Xu, X., Zhang, H., Xi, Z., Abbott, R. J., Fu, J., & Liu, J.
(2022). Abiotic Niche Divergence of Hybrid Species from Their
Progenitors. The American naturalist , 200 (5), 634–645.
https://doi.org/10.1086/721372
Wang, Z., Jiang, Y., Bi, H., Lu, Z., Ma, Y., Yang, X., Chen, N., Tian,
B., Liu, B., Mao, X., Ma, T., DiFazio, S. P., Hu, Q., Abbott, R. J., &
Liu, J. (2021). Hybrid speciation via inheritance of alternate alleles
of parental isolating genes. Molecular plant , 14 (2),
208–222. https://doi.org/10.1016/j.molp.2020.11.008
Wang, Z., Kang, M., Li, J., Zhang, Z., Wang, Y., Chen, C., Yang, Y., &
Liu, J. (2022). Genomic evidence for homoploid hybrid speciation between
ancestors of two different genera. Nature
communications , 13 (1), 1987.
https://doi.org/10.1038/s41467-022-29643-4
Wogan, G. O. U., Yuan, M. L., Mahler, D. L., & Wang, I. J. (2023).
Hybridization and Transgressive Evolution Generate Diversity in an
Adaptive Radiation of Anolis Lizards. Systematic
biology , 72 (4), 874–884. https://doi.org/10.1093/sysbio/syad026
Wood, T. E., Takebayashi, N., Barker, M. S., Mayrose, I., Greenspoon, P.
B., & Rieseberg, L. H. (2009). The frequency of polyploid speciation in
vascular plants. Proceedings of the National Academy of Sciences
of the United States of America , 106 (33), 13875–13879.
https://doi.org/10.1073/pnas.0811575106
Wu, H., Wang, Z., Zhang, Y., Frantz, L., Roos, C., Irwin, D. M., Zhang,
C., Liu, X., Wu, D., Huang, S., Gu, T., Liu, J., & Yu, L. (2023).
Hybrid origin of a primate, the gray snub-nosed monkey. Science
(New York, N.Y.) , 380 (6648), eabl4997.
https://doi.org/10.1126/science.abl4997 Zalmat et al., 2021;
Y C Brandt, D., Wei, X., Deng, Y., Vaughn, A. H., & Nielsen, R. (2022).
Evaluation of methods for estimating coalescence times using ancestral
recombination graphs. Genetics , 221 (1), iyac044.
https://doi.org/10.1093/genetics/iyac044.
Zhang, B. L., Chen, W., Wang, Z., Pang, W., Luo, M. T., Wang, S., Shao,
Y., He, W. Q., Deng, Y., Zhou, L., Chen, J., Yang, M. M., Wu, Y., Wang,
L., Fernández-Bellon, H., Molloy, S., Meunier, H., Wanert, F., Kuderna,
L., Marques-Bonet, T., … Wu, D. D. (2023). Comparative genomics
reveals the hybrid origin of a macaque group. Science
advances , 9 (22), eadd3580.
https://doi.org/10.1126/sciadv.add3580
Zou, T., Kuang, W., Yin, T., Frantz, L., Zhang, C., Liu, J., Wu, H., &
Yu, L. (2022). Uncovering the enigmatic evolution of bears in greater
depth: The hybrid origin of the Asiatic black bear. Proceedings of
the National Academy of Sciences of the United States of
America , 119 (31), e2120307119.
https://doi.org/10.1073/pnas.2120307119