Phylogenomics reveals three sources of adaptive variation during a rapid radiation
Open accessAbstract
Speciation events often occur in rapid bursts of diversification, but the ecological and genetic factors that promote these radiations are still much debated. Using whole transcriptomes from all 13 species in the ecologically and reproductively diverse wild tomato clade (Solanum sect. Lycopersicon), we infer the species phylogeny and patterns of genetic diversity in this group. Despite widespread phylogenetic discordance due to the sorting of ancestral variation, we date the origin of this radiation to approximately 2.5 million years ago and find evidence for at least three sources of adaptive genetic variation that fuel diversification. First, we detect introgression both historically between early-branching lineages and recently between individual populations, at specific loci whose functions indicate likely adaptive benefits. Second, we find evidence of lineage-specific de novo evolution for many genes, including loci involved in the production of red fruit color. Finally, using a "PhyloGWAS" approach, we detect environment-specific sorting of ancestral variation among populations that come from different species but share common environmental conditions. Estimated across the whole clade, small but substantial and approximately equal fractions of the euchromatic portion of the genome are inferred to contribute to each of these three sources of adaptive genetic variation. These results indicate that multiple genetic sources can promote rapid diversification and speciation in response to new ecological opportunity, in agreement with our emerging phylogenomic understanding of the complexity of both ancient and recent species radiations.
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In the wild tomato clade (Solanum section Lycopersicon), ancestral standing variation, introgression, and new mutations have contributed approximately equally to this recent adaptive radiation.
“This is illustrated by analyses of the wild tomato clade (Solanum section Lycopersicon), in which ancestral standing variation, introgression, and new mutations have contributed approximately equally to this recent adaptive radiation (Pease et al., 2016).”
From Genomics of plant speciation (2023) · cites this paper as Pease et al., 2016
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Cites
The Sequence Alignment/Map format and SAMtools
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041 · see citing works
STAR: ultrafast universal RNA-seq aligner
Dobin, A., Davis, C. A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., Batut, P., Chaisson, M., & Gingeras, T. R. (2013) · Bioinformatics · doi:10.1093/bioinformatics/bts635 · Cited by 51,709 · see citing works
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
Stamatakis, A. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu033 · Cited by 32,291 · see citing works
PAML 4: Phylogenetic Analysis by Maximum Likelihood
Yang, Z. (2007) · Molecular Biology and Evolution · doi:10.1093/molbev/msm088 · Cited by 13,879 · see citing works
The Ecology of Adaptive Radiation
Schluter, D. (2000) · doi:10.1093/oso/9780198505235.001.0001 · Cited by 4,974 · see citing works
A draft sequence of the Neandertal genome
Green, R. E., Krause, J., Briggs, A. W., Maricic, T., Stenzel, U., Kircher, M., Patterson, N., Li, H., Zhai, W., Fritz, M. H.-Y., et al. (2010) · Science · doi:10.1126/science.1188021 · Cited by 4,318 · see citing works
The tomato genome sequence provides insights into fleshy fruit evolution
Hirakawa, H., Asamizu, E., Shirasawa, K., Isobe, S., Kaneko, T., Nakamura, Y., Shibata, D., Aoki, K., Egholm, M., Knight, J. R., et al. (2012) · Nature · doi:10.1038/nature11119 · Cited by 3,294 · see citing works
Amazonia Through Time: Andean Uplift, Climate Change, Landscape Evolution, and Biodiversity
Hoorn, C., Wesselingh, F. P., ter Steege, H., Bermudez, M. A., Mora, A., Sevink, J., Sanmartín, I., Sanchez-Meseguer, A., Anderson, C. L., Figueiredo, J. P., et al. (2010) · Science · doi:10.1126/science.1194585 · Cited by 2,404 · see citing works
Generating samples under a Wright–Fisher neutral model of genetic variation
Hudson, R. R. (2002) · Bioinformatics · doi:10.1093/bioinformatics/18.2.337 · Cited by 2,397 · see citing works
Genome sequence and analysis of the tuber crop potato
Xu, X., Pan, S., Cheng, S., Zhang, B., Mu, D., Ni, P., Zhang, G., Guzman, F., Torres, M., Lozano, R., et al. (2011) · Nature · doi:10.1038/nature10158 · Cited by 2,050 · see citing works
Sanderson, M. J. (2003) · Bioinformatics · doi:10.1093/bioinformatics/19.2.301 · Cited by 1,906 · see citing works
Whole-genome analyses resolve early branches in the tree of life of modern birds
Jarvis, E. D., Mirarab, S., Aberer, A. J., Li, B., Houde, P., Li, C., Ho, S. Y. W., Faircloth, B. C., Nabholz, B., Howard, J. T., et al. (2014) · Science · doi:10.1126/science.1253451 · Cited by 1,901 · see citing works
Hybridization and adaptive radiation
D, O. S. C. (2004) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2004.01.003 · Cited by 1,861 · see citing works
Natural Hybridization and Evolution
Arnold, M. L. (1997) · doi:10.1093/oso/9780195099744.001.0001 · Cited by 1,784 · see citing works
Natural hybridization and evolution
(1997) · Choice Reviews Online · doi:10.5860/choice.35-0883 · Cited by 1,742 · see citing works
Relationships between gene trees and species trees.
Pamilo, P., & Nei, M. (1988) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a040517 · Cited by 1,652 · see citing works
Widespread parallel evolution in sticklebacks by repeated fixation of Ectodysplasin alleles.
Colosimo, P. F., Hosemann, K. E., Balabhadra, S., Villarreal, G., Dickson, M., Grimwood, J., Schmutz, J., Myers, R. M., Schluter, D., & Kingsley, D. M. (2005) · Science · doi:10.1126/science.1107239 · Cited by 1,448 · see citing works
Testing for ancient admixture between closely related populations
Durand, E. Y., Patterson, N., Reich, D., & Slatkin, M. (2011) · Molecular Biology and Evolution · doi:10.1093/molbev/msr048 · Cited by 1,375 · see citing works
ASTRAL: genome-scale coalescent-based species tree estimation
Mirarab, S., Reaz, R., Bayzid, M. S., Zimmermann, T., Swenson, M. S., & Warnow, T. J. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu462 · Cited by 1,312 · see citing works
Phylotranscriptomic analysis of the origin and early diversification of land plants
Wickett, N. J., Mirarab, S., Nguyen, N., Warnow, T., Carpenter, E., Matasci, N., Ayyampalayam, S., Barker, M. S., Burleigh, J. G., Gitzendanner, M. A., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1323926111 · Cited by 1,252 · see citing works
Evolution of Darwin’s finches and their beaks revealed by genome sequencing
Lamichhaney, S., Berglund, J., Almén, M. S., Maqbool, K., Grabherr, M. G., Barrio, Á. M., Promerová, M., Rubin, C., Wang, C., Zamani, N., et al. (2015) · Nature · doi:10.1038/nature14181 · Cited by 990 · see citing works
The genomic substrate for adaptive radiation in African cichlid fish
Brawand, D., Wagner, C. E., Li, Y., Malinsky, M., Keller, I., Fan, S., Simakov, O., Ng, A. Y. J., Lim, Z. W., Bezault, É., et al. (2014) · Nature · doi:10.1038/nature13726 · Cited by 989 · see citing works
Adaptive evolution in invasive species
Prentis, P. J., Wilson, J. R., Dormontt, E. E., Richardson, D. M., & Lowe, A. J. (2008) · Trends in Plant Science · doi:10.1016/j.tplants.2008.03.004 · Cited by 953 · see citing works
Genomic analyses provide insights into the history of tomato breeding
Lin, T., Zhu, G., Zhang, J., Xu, X., Yu, Q., Zheng, Z., Zhang, Z., Lun, Y., Li, S., Wang, X., et al. (2014) · Nature Genetics · doi:10.1038/ng.3117 · Cited by 950 · see citing works
Adaptive radiation: Contrasting theory with data
Gavrilets, S., & Losos, J. B. (2009) · Science · doi:10.1126/science.1157966 · Cited by 750 · see citing works
Evaluating the Use of ABBA–BABA Statistics to Locate Introgressed Loci
Martin, S. H., Davey, J. W., & Jiggins, C. D. (2014) · Molecular Biology and Evolution · doi:10.1093/molbev/msu269 · Cited by 722 · see citing works
Hedrick, P. W. (2013) · Molecular Ecology · doi:10.1111/mec.12415 · Cited by 695 · see citing works
The Biology and Taxonomy of the Solanaceae.
Correll, D. S., Hawkes, J. G., Lester, R. N., & Skelding, A. D. (1980) · Systematic Botany · doi:10.2307/2418380 · Cited by 671 · see citing works
Garzione, C. N., Hoke, G. D., Libarkin, J. C., Withers, S., MacFadden, B. J., Eiler, J. M., Ghosh, P., & Mulch, A. (2008) · Science · doi:10.1126/science.1148615 · Cited by 655 · see citing works
Domestication and Breeding of Tomatoes: What have We Gained and What Can We Gain in the Future?
Bai, Y., & Lindhout, P. (2007) · Annals of Botany · doi:10.1093/aob/mcm150 · Cited by 648 · see citing works
The Ecology of Adaptive Radiation
Turner, G. F. (2001) · Heredity · doi:10.1046/j.1365-2540.2001.0947b.x · Cited by 647 · see citing works
Genome-wide evidence for speciation with gene flow in Heliconius butterfliesPreprint
Martin, S. H., Dasmahapatra, K. K., Nadeau, N. J., Salazar, C. A., Walters, J. R., Simpson, F., Blaxter, M., Manica, A., Mallet, J., & Jiggins, C. D. (2013) · Genome Research · doi:10.1101/gr.159426.113 · Cited by 640 · see citing works
Extensive introgression in a malaria vector species complex revealed by phylogenomics
Fontaine, M. C., Pease, J. B., Steele, A., Waterhouse, R. M., Neafsey, D. E., Sharakhov, I. V., Jiang, X., Hall, A. B., Catteruccia, F., Kakani, E. G., et al. (2014) · Science · doi:10.1126/science.1258524 · Cited by 630 · see citing works
Self-citationInferring ancient divergences requires genes with strong phylogenetic signals
Salichos, L., & Rokas, A. (2013) · Nature · doi:10.1038/nature12130 · Cited by 616 · see citing works
A maximum pseudo-likelihood approach for estimating species trees under the coalescent model
Liu, L., Yu, L., & Edwards, S. V. (2010) · BMC Evolutionary Biology · doi:10.1186/1471-2148-10-302 · Cited by 607 · see citing works
Wild Crop Relatives: Genomic and Breeding Resources
Bhattacharya, A., Rice, N., Shapter, F. M., Norton, S. L., & Henry, R. J. (2011) · Springer eBooks · doi:10.1007/978-3-642-14228-4 · Cited by 599 · see citing works
Särkinen, T., Bohs, L., Olmstead, R. G., & Knapp, S. (2013) · BMC Evolutionary Biology · doi:10.1186/1471-2148-13-214 · Cited by 550 · see citing works
Ecological opportunity and sexual selection together predict adaptive radiation
Wagner, C. E., Harmon, L. J., & D, O. S. C. (2012) · Nature · doi:10.1038/nature11144 · Cited by 500 · see citing works
Loss of Self‐Incompatibility and Its Evolutionary Consequences
Igić, B., Lande, R., & Kohn, J. R. (2008) · International Journal of Plant Sciences · doi:10.1086/523362 · Cited by 455 · see citing works
Aflitos, S. A., Schijlen, E. G. W. M., de Jong, H., de Ridder, D., Smit, S., Finkers, R., Wang, J., Zhang, G., Li, N., Mao, L., et al. (2014) · The Plant Journal · doi:10.1111/tpj.12616 · Cited by 414 · see citing works
Pruning Rogue Taxa Improves Phylogenetic Accuracy: An Efficient Algorithm and Webservice
Aberer, A. J., Krompaß, D., & Stamatakis, A. (2012) · Systematic Biology · doi:10.1093/sysbio/sys078 · Cited by 401 · see citing works
Developmental Genetics and Plant Evolution
Cronk, Q., Bateman, R. M., & Hawkins, J. A. (2004) · CRC Press eBooks · doi:10.1201/9781420024982 · Cited by 371 · see citing works
Gibbon genome and the fast karyotype evolution of small apes
Carbone, L., Harris, R. A., Gnerre, S., Veeramah, K. R., Lorente-Galdós, B., Huddleston, J., Meyer, T. J., Herrero, J., Roos, C., Aken, B. L., et al. (2014) · Nature · doi:10.1038/nature13679 · Cited by 360 · see citing works
Self-citationPhylogenetic Insights on Adaptive Radiation
Glor, R. E. (2010) · Annual Review of Ecology Evolution and Systematics · doi:10.1146/annurev.ecolsys.39.110707.173447 · Cited by 355 · see citing works
Tobacco to tomatoes: a phylogenetic perspective on fruit diversity in the Solanaceae
Knapp, S. (2002) · Journal of Experimental Botany · doi:10.1093/jxb/erf068 · Cited by 329 · see citing works
Development of a Large SNP Genotyping Array and Generation of High-Density Genetic Maps in Tomato
Sim, S., Durstewitz, G., Plieske, J., Wieseke, R., Ganal, M. W., Deynze, A. V., Hamilton, J. P., Buell, C. R., Causse, M., Wijeratne, S., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0040563 · Cited by 316 · see citing works
Phylogenetic insights into Andean plant diversification
Luebert, F., & Weigend, M. (2014) · Frontiers in Ecology and Evolution · doi:10.3389/fevo.2014.00027 · Cited by 306 · see citing works
150 million years of climatic stability: evidence from the Atacama Desert, northern Chile
Hartley, A. J., Chong, G., Houston, J., & Mather, A. E. (2005) · Journal of the Geological Society · doi:10.1144/0016-764904-071 · Cited by 301 · see citing works
Chloroplast DNA evolution and phylogenetic relationships in Lycopersicon
Palmer, J. D., & Zamir, D. (1982) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.79.16.5006 · Cited by 292 · see citing works
TESTING THE CONSTANT-RATE NEUTRAL ALLELE MODEL WITH PROTEIN SEQUENCE DATA
Hudson, R. R. (1983) · Evolution · doi:10.1111/j.1558-5646.1983.tb05528.x · Cited by 289 · see citing works
The Dynamics of Incomplete Lineage Sorting across the Ancient Adaptive Radiation of Neoavian Birds
Suh, A., Smeds, L., & Ellegren, H. (2015) · PLoS Biology · doi:10.1371/journal.pbio.1002224 · Cited by 275 · see citing works
Diversity-dependence, ecological speciation, and the role of competition in macroevolution
Rabosky, D. L. (2013) · Annual Review of Ecology Evolution and Systematics · doi:10.1146/annurev-ecolsys-110512-135800 · Cited by 268 · see citing works
Detection and Polarization of Introgression in a Five-Taxon Phylogeny
Pease, J. B., & Hahn, M. W. (2015) · Systematic Biology · doi:10.1093/sysbio/syv023 · Cited by 268 · see citing works
Self-citationEcological and geographic modes of species divergence in wild tomatoes
Nakazato, T., Warren, D. L., & Moyle, L. C. (2010) · American Journal of Botany · doi:10.3732/ajb.0900216 · Cited by 256 · see citing works
Self-citationA Three-Gene Phylogeny of the Genus Solanum (Solanaceae)
Weese, T. L., & Bohs, L. (2007) · Systematic Botany · doi:10.1600/036364407781179671 · Cited by 256 · see citing works
Dissection of Tomato Lycopene Biosynthesis through Virus-Induced Gene Silencing
Fantini, E., Falcone, G., Frusciante, S., Giliberto, L., & Giuliano, G. (2013) · PLANT PHYSIOLOGY · doi:10.1104/pp.113.224733 · Cited by 249 · see citing works
Equilibrium speciation dynamics in a model adaptive radiation of island lizards
Rabosky, D. L., & Glor, R. E. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1007606107 · Cited by 242 · see citing works
Confluence, synnovation, and depauperons in plant diversification
Donoghue, M. J., & Sanderson, M. J. (2015) · New Phytologist · doi:10.1111/nph.13367 · Cited by 234 · see citing works
Peralta, I. E., Spooner, D. M., & Knapp, S. (2008) · Systematic Botany Monographs · Cited by 221 · see citing works
Speciation with gene flow in equids despite extensive chromosomal plasticity
Jónsson, H., Schubert, M., Seguin‐Orlando, A., Ginolhac, A., Petersen, L., Fumagalli, M., Albrechtsen, A., Petersen, B., Korneliussen, T. S., Vilstrup, J. T., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1412627111 · Cited by 219 · see citing works
Hybrid Incompatibility “Snowballs” Between <i>Solanum</i> Species
Moyle, L. C., & Nakazato, T. (2010) · Science · doi:10.1126/science.1193063 · Cited by 217 · see citing works
Self-citationMolecular Interactions Between Tomato and the Leaf Mold Pathogen Cladosporium fulvum
Rivas, S., & Thomas, C. M. (2005) · Annual Review of Phytopathology · doi:10.1146/annurev.phyto.43.040204.140224 · Cited by 212 · see citing works
Testing the Constant-Rate Neutral Allele Model with Protein Sequence Data
Hudson, R. R. (1983) · Evolution · doi:10.2307/2408186 · Cited by 209 · see citing works
Genome sequencing reveals complex speciation in the Drosophila simulans cladePreprint
Garrigan, D., Kingan, S. B., Geneva, A. J., Andolfatto, P., Clark, A. G., Thornton, K., & Presgraves, D. C. (2012) · Genome Research · doi:10.1101/gr.130922.111 · Cited by 203 · see citing works
New Species of Wild Tomatoes (Solanum Section Lycopersicon: Solanaceae) from Northern Peru
Peralta, I. E., Knapp, S., & Spooner, D. M. (2005) · Systematic Botany · doi:10.1600/0363644054223657 · Cited by 203 · see citing works
Yang, Y. J., Moore, M. J., Brockington, S. F., Soltis, P. S., Wong, G. K., Carpenter, E. J., Zhang, Y., Chen, L., Yan, Z., Xie, Y., et al. (2015) · Molecular Biology and Evolution · doi:10.1093/molbev/msv081 · Cited by 199 · see citing works
Andean uplift, ocean cooling and Atacama hyperaridity: a climate modeling perspective
Garreaud, R. D., Molina, A., & Farias, M. (2010) · Earth and Planetary Science Letters · doi:10.1016/j.epsl.2010.01.017 · Cited by 199 · see citing works
Adaptive introgression of abiotic tolerance traits in the sunflower Helianthus annuus
Whitney, K. D., Randell, R. A., & Rieseberg, L. H. (2010) · New Phytologist · doi:10.1111/j.1469-8137.2010.03234.x · Cited by 198 · see citing works
Clade Age and Species Richness Are Decoupled Across the Eukaryotic Tree of Life
Rabosky, D. L., Slater, G. J., & Alfaro, M. E. (2012) · PLoS Biology · doi:10.1371/journal.pbio.1001381 · Cited by 197 · see citing works
Gene tree discordance causes apparent substitution rate variation
Mendes, F. K., & Hahn, M. W. (2016) · Systematic Biology · doi:10.1093/sysbio/syw018 · Cited by 189 · see citing works
Self-citationPlant carotenoids: genomics meets multi-gene engineering
Giuliano, G. A. (2014) · Current Opinion in Plant Biology · doi:10.1016/j.pbi.2014.05.006 · Cited by 172 · see citing works
PHYLOGENOMICS REVEALS EXTENSIVE RETICULATE EVOLUTION INXIPHOPHORUSFISHES
Cui, R., Schumer, M. E., Kruesi, K., Walter, R. B., Andolfatto, P., & Rosenthal, G. G. (2013) · Evolution · doi:10.1111/evo.12099 · Cited by 170 · see citing works
D, O. S. C. (2015) · New Phytologist · doi:10.1111/nph.13450 · Cited by 168 · see citing works
Compatibility and incompatibility in S-RNase-based systems
McClure, B., Cruz‐García, F., & Romero, C. (2011) · Annals of Botany · doi:10.1093/aob/mcr179 · Cited by 168 · see citing works
Hiller, M., Schaar, B. T., Indjeian, V. B., Kingsley, D. M., Hagey, L. R., & Bejerano, G. (2012) · Cell Reports · doi:10.1016/j.celrep.2012.08.032 · Cited by 144 · see citing works
Garzione, C. N., Auerbach, D. J., Jin-Sook Smith, J., Rosario, J. J., Passey, B. H., Jordan, T. E., & Eiler, J. M. (2014) · Earth and Planetary Science Letters · doi:10.1016/j.epsl.2014.02.029 · Cited by 127 · see citing works
Introgressive hybridization facilitates adaptive divergence in a recent radiation of monkeyflowers
Stankowski, S., & Streisfeld, M. A. (2015) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2015.1666 · Cited by 113 · see citing works
Arnold, M. L., & Martin, N. H. (2009) · Journal of Biology · doi:10.1186/jbiol176 · Cited by 110 · see citing works
ECOLOGICAL AND EVOLUTIONARY GENOMICS IN THE WILD TOMATOES (SOLANUM SECT. LYCOPERSICON)
Moyle, L. C. (2008) · Evolution · doi:10.1111/j.1558-5646.2008.00487.x · Cited by 109 · see citing works
Self-citationResource polyphenism increases species richness: a test of the hypothesis
Pfennig, D. W., & McGee, M. D. (2010) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2009.0244 · Cited by 109 · see citing works
Rodríguez, F., Wu, F., Ané, C., Tanksley, S. D., & Spooner, D. M. (2009) · BMC Evolutionary Biology · doi:10.1186/1471-2148-9-191 · Cited by 106 · see citing works
Baute, G. J., Kane, N. C., Grassa, C. J., Lai, Z., & Rieseberg, L. H. (2015) · New Phytologist · doi:10.1111/nph.13255 · Cited by 97 · see citing works
Xu, J., Ranc, N., Muños, S., Rolland, S., Bouchet, J., Desplat, N., Paslier, M. L., Liang, Y., Brunel, D., & Causse, M. (2012) · Theoretical and Applied Genetics · doi:10.1007/s00122-012-2002-8 · Cited by 96 · see citing works
Verlaan, M. G., Szinay, D., Hutton, S. F., de Jong, H., Kormelink, R., Visser, R. G. F., Scott, J. W., & Bai, Y. (2011) · The Plant Journal · doi:10.1111/j.1365-313x.2011.04762.x · Cited by 94 · see citing works
Ranc, N., Muños, S., Xu, J., Paslier, M. L., Chauveau, A., Bounon, R., Rolland, S., Bouchet, J., Brunel, D., & Causse, M. (2012) · G3 Genes Genomes Genetics · doi:10.1534/g3.112.002667 · Cited by 91 · see citing works
Dillon, M. O., Tu, T., Xie, L., Silvestre, V. Q., & Wen, J. (2009) · Journal of Systematics and Evolution · doi:10.1111/j.1759-6831.2009.00040.x · Cited by 89 · see citing works
Shearer, L. A., Anderson, L. K., de Jong, H., Smit, S., Goicoechea, J. L., Roe, B. A., Hua, A., Giovannoni, J. J., & Stack, S. M. (2014) · G3 Genes Genomes Genetics · doi:10.1534/g3.114.011197 · Cited by 88 · see citing works
The involvement of chloroplast HSP100/ClpB in the acquired thermotolerance in tomato
Yang, J., Sun, Y., Sun, A.-Q., Yi, S., Qin, J., Li, M., & Liu, J. (2006) · Plant Molecular Biology · doi:10.1007/s11103-006-9027-9 · Cited by 87 · see citing works
Picard, D., Sempéré, T., & Plantard, O. (2008) · Earth and Planetary Science Letters · doi:10.1016/j.epsl.2008.04.024 · Cited by 84 · see citing works
Baek, Y. S., Covey, P. A., Petersen, J. J., Chetelat, R. T., McClure, B., & Bedinger, P. A. (2015) · American Journal of Botany · doi:10.3732/ajb.1400484 · Cited by 79 · see citing works
Doan, T. M. (2003) · Journal of Biogeography · doi:10.1046/j.1365-2699.2003.00833.x · Cited by 76 · see citing works
Chromosome evolution in Solanum traced by cross‐species BAC‐FISH
Szinay, D., Wijnker, T. G., van den Berg, R., Visser, R. G. F., de Jong, H., & Bai, Y. (2012) · New Phytologist · doi:10.1111/j.1469-8137.2012.04195.x · Cited by 64 · see citing works
Thinking in continua: beyond the “adaptive radiation” metaphor
Olson, M. E., & Arroyo‐Santos, A. (2009) · BioEssays · doi:10.1002/bies.200900102 · Cited by 61 · see citing works
Sequence diversity in three tomato species: SNPs, markers, and molecular evolution
Jiménez‐Gómez, J. M., & Maloof, J. (2009) · BMC Plant Biology · doi:10.1186/1471-2229-9-85 · Cited by 56 · see citing works
Grandillo, S., Chetelat, R. T., Knapp, S., Spooner, D. M., Peralta, I. E., Cammareri, M., Perez, O., Termolino, P., Tripodi, P., Chiusano, M. L., et al. (2011) · Springer eBooks · doi:10.1007/978-3-642-20450-0_9 · Cited by 56 · see citing works
Wild Crop Relatives: Genomic and Breeding Resources
Kole, C. (2011) · Springer eBooks · doi:10.1007/978-3-642-16057-8 · Cited by 52 · see citing works
The Cf-4 and Cf-9 Resistance Genes Against Cladosporium fulvum are Conserved in Wild Tomato Species
Kruijt, M., Kip, D. J., JOOSTEN, M. H. A. J., Brandwagt, B. F., & WIT, P. J. G. M. D. (2005) · Molecular Plant-Microbe Interactions · doi:10.1094/mpmi-18-1011 · Cited by 50 · see citing works
Structural Differences in Chromosomes Distinguish Species in the Tomato Clade
Anderson, L. K., Covey, P. A., Larsen, L. R., Bedinger, P. A., & Stack, S. M. (2010) · Cytogenetic and Genome Research · doi:10.1159/000313850 · Cited by 49 · see citing works
Floral diversity and evolution in the Solanaceae
Knapp, S. (2002) · Systematics Association special volume · doi:10.1201/9781420024982.ch14 · Cited by 46 · see citing works
Genetic structure of the four wild tomato species in theSolanum peruvianums.l. species complex
Labate, J. A., Robertson, L. D., Strickler, S. R., & Mueller, L. A. (2014) · Genome · doi:10.1139/gen-2014-0003 · Cited by 27 · see citing works
Pease, J. B., & Rosenzweig, B. K. (2015) · IEEE Transactions on Computational Biology and Bioinformatics · doi:10.1109/tcbb.2015.2509997 · Cited by 27 · see citing works
Self-citationMorphological characterization and relationships of wild tomatoes (Solanum L. sect. Lycopersicon)
Peralta, I. E. (2005) · Cited by 22 · see citing works
Vosters, S. L., Jewell, C. P., Sherman, N. A., Einterz, F., Blackman, B. K., & Moyle, L. C. (2014) · Molecular Ecology · doi:10.1111/mec.12708 · Cited by 21 · see citing works
Self-citationData from: Phylogenomics reveals three sources of adaptive variation during a rapid radiation
Pease, J. B., Haak, D. C., Hahn, M. W., & Moyle, L. C. (2016) · Data Archiving and Networked Services (DANS) · doi:10.5061/dryad.182dv · Cited by 1 · see citing works
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Genomic architecture and introgression shape a butterfly radiation
Edelman, N. B., Frandsen, P. B., Miyagi, M., Clavijo, B., Davey, J. W., Dikow, R. B., Accinelli, G. G., Belleghem, S. M. V., Patterson, N. J., Neafsey, D. E., et al. (2019) · Science · doi:10.1126/science.aaw2090 · Cited by 588 · see citing works
A Combinatorial View on Speciation and Adaptive Radiation
Marques, D. A., Meier, J. I., & D, O. S. C. (2019) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2019.02.008 · Cited by 562 · see citing works
Stein, J. C., Yu, Y., Copetti, D., Zwickl, D. J., Zhang, L., Zhang, C., Chougule, K. M., Gao, D., Iwata‐Otsubo, A., Goicoechea, J. L., et al. (2018) · Nature Genetics · doi:10.1038/s41588-018-0040-0 · Cited by 561 · see citing works
Variation in the flowering gene SELF PRUNING 5G promotes day-neutrality and early yield in tomato
Soyk, S., Müller, N. A., Park, S. J., Schmalenbach, I., Jiang, K., Hayama, R., Zhang, L., Eck, J. M. V., Jiménez‐Gómez, J. M., & Lippman, Z. B. (2016) · Nature Genetics · doi:10.1038/ng.3733 · Cited by 465 · see citing works
Hybridization in Plants: Old Ideas, New Techniques
Goulet‐Scott, B. E., Roda, F., & Hopkins, R. (2016) · PLANT PHYSIOLOGY · doi:10.1104/pp.16.01340 · Cited by 355 · see citing works
Pease, J. B., Brown, J. W., Walker, J. F., Hinchliff, C. E., & Smith, S. A. (2018) · American Journal of Botany · doi:10.1002/ajb2.1016 · Cited by 334 · see citing works
Self-citationWidespread introgression across a phylogeny of 155 Drosophila genomes
Suvorov, A., Kim, B. Y., Wang, J., Armstrong, E. E., Peede, D., D’Agostino, E. R. R., Price, D. K., Waddell, P. J., Lang, M., Courtier‐Orgogozo, V., et al. (2021) · Current Biology · doi:10.1016/j.cub.2021.10.052 · Cited by 260 · see citing works
Prevalence and Adaptive Impact of Introgression
Edelman, N. B., & Mallet, J. (2021) · Annual Review of Genetics · doi:10.1146/annurev-genet-021821-020805 · Cited by 239 · see citing works
Phylogenomic approaches to detecting and characterizing introgression
Hibbins, M. S., & Hahn, M. W. (2021) · Genetics · doi:10.1093/genetics/iyab173 · Cited by 222 · see citing works
Self-citationLocal PCA Shows How the Effect of Population Structure Differs Along the Genome
Li, H., & Ralph, P. L. (2018) · Genetics · doi:10.1534/genetics.118.301747 · Cited by 210 · see citing works
PhyKIT: a broadly applicable UNIX shell toolkit for processing and analyzing phylogenomic data
Steenwyk, J. L., Buida, T. J., LaBella, A. L., Li, Y., Shen, X., & Rokas, A. (2021) · Bioinformatics · doi:10.1093/bioinformatics/btab096 · Cited by 205 · see citing works
De Novo Assembly of a New Solanum pennellii Accession Using Nanopore Sequencing
Schmidt, M., Vogel, A., Denton, A. K., Istace, B., Wormit, A., van de Geest, H., Bolger, M., Alseekh, S., Maß, J., Pfaff, C., et al. (2017) · The Plant Cell · doi:10.1105/tpc.17.00521 · Cited by 202 · see citing works
The evolutionary genomics of species’ responses to climate change
Aguirre‐Liguori, J. A., Ramírez‐Barahona, S., & Gaut, B. S. (2021) · Nature Ecology & Evolution · doi:10.1038/s41559-021-01526-9 · Cited by 197 · see citing works
Practical considerations for plant phylogenomics
McKain, M. R., Johnson, M. G., Uribe‐Convers, S., Eaton, D. A. R., & Yang, Y. J. (2018) · Applications in Plant Sciences · doi:10.1002/aps3.1038 · Cited by 193 · see citing works
Stein, R. J., Höreth, S., de Melo, J. R. F., Syllwasschy, L., Lee, G., Garbin, M. L., Clemens, S., & Krämer, U. (2016) · New Phytologist · doi:10.1111/nph.14219 · Cited by 188 · see citing works
Fan, H., Lamichhaney, S., Grant, B. R., Grant, P. R., Andersson, L., & Webster, M. T. (2017) · Genome Research · doi:10.1101/gr.212522.116 · Cited by 188 · see citing works
Irrational exuberance for resolved species trees: COMMENTARY
Hahn, M. W., & Nakhleh, L. (2016) · Evolution · doi:10.1111/evo.12832 · Cited by 187 · see citing works
Self-citationCai, L., Xi, Z., Lemmon, E. M., Lemmon, A. R., Mast, A., Buddenhagen, C. E., Liu, L., & Davis, C. “. (2020) · Systematic Biology · doi:10.1093/sysbio/syaa083 · Cited by 180 · see citing works
Novikova, P. Y., Hohmann, N., Nizhynska, V., Tsuchimatsu, T., Ali, J., Muir, G., Guggisberg, A., Paape, T. D., Schmid, K., Федоренко, О. М., et al. (2016) · Nature Genetics · doi:10.1038/ng.3617 · Cited by 179 · see citing works
Genomics of Evolutionary Novelty in Hybrids and Polyploids
Feliner, G. N., Casacuberta, J., & Wendel, J. F. (2020) · Frontiers in Genetics · doi:10.3389/fgene.2020.00792 · Cited by 154 · see citing works
Incomplete lineage sorting and phenotypic evolution in marsupials
Feng, S., Bai, M., Rivas-González, I., Li, C., Liu, S., Tong, Y., Yang, H., Chen, G., Xie, D., Sears, K. E., et al. (2022) · Cell · doi:10.1016/j.cell.2022.03.034 · Cited by 150 · see citing works
Meleshko, O., Martin, M. D., Korneliussen, T. S., Schröck, C., Lamkowski, P., Schmutz, J., Healey, A. L., Piatkowski, B. T., Shaw, A. J., Weston, D. J., et al. (2021) · Molecular Biology and Evolution · doi:10.1093/molbev/msab063 · Cited by 148 · see citing works
Phylogenomics and the flowering plant tree of life
Guo, C., Luo, Y., Gao, L., Yi, T., Li, H., Yang, J., & Li, D.-Z. (2022) · Journal of Integrative Plant Biology · doi:10.1111/jipb.13415 · Cited by 148 · see citing works
Challenges in Species Tree Estimation Under the Multispecies Coalescent Model
Xu, B., & Yang, Z. (2016) · Genetics · doi:10.1534/genetics.116.190173 · Cited by 147 · see citing works
New prospects in the detection and comparative analysis of hybridization in the tree of life
Folk, R. A., Soltis, P. S., Soltis, P. S., & Guralnick, R. (2018) · American Journal of Botany · doi:10.1002/ajb2.1018 · Cited by 145 · see citing works
Embracing heterogeneity: coalescing the Tree of Life and the future of phylogenomics
Bravo, G. A., Antonelli, A., Bacon, C. D., Bartoszek, K., Blom, M. P. K., Huynh, S., Jones, G., Knowles, L. L., Lamichhaney, S., Marcussen, T., et al. (2019) · PeerJ · doi:10.7717/peerj.6399 · Cited by 143 · see citing works
Filiault, D. L., Ballerini, E. S., Mandáková, T. M., Aköz, G., Derieg, N. J., Schmutz, J., Jenkins, J. W., Grimwood, J., Shu, S., Hayes, R. D., et al. (2018) · eLife · doi:10.7554/elife.36426 · Cited by 143 · see citing works
Phylogenetics is the New Genetics (for Most of Biodiversity)
Smith, S., Pennell, M. W., Dunn, C. W., & Edwards, S. V. (2020) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2020.01.005 · Cited by 139 · see citing works
Phylogenomic discovery of deleterious mutations facilitates hybrid potato breeding
Wu, Y., Li, D., Hu, Y., Li, H., Ramstein, G. P., Zhou, S., Zhang, X., Bao, Z., Zhang, Y., Song, B., et al. (2023) · Cell · doi:10.1016/j.cell.2023.04.008 · Cited by 135 · see citing works
The phylogenomic forest of bird trees contains a hard polytomy at the root of Neoaves
Suh, A. (2016) · Zoologica Scripta · doi:10.1111/zsc.12213 · Cited by 134 · see citing works
Widespread selection and gene flow shape the genomic landscape during a radiation of monkeyflowers
Stankowski, S., Chase, M. A., Fuiten, A. M., Rodrigues, M. F., Ralph, P. L., & Streisfeld, M. A. (2019) · PLOS Biology · doi:10.1371/journal.pbio.3000391 · Cited by 134 · see citing works
Ancient genomic variation underlies repeated ecological adaptation in young stickleback populations
Nelson, T. C., & Cresko, W. A. (2018) · Evolution Letters · doi:10.1002/evl3.37 · Cited by 132 · see citing works
Adaptive Genetic Exchange: A Tangled History of Admixture and Evolutionary Innovation
Arnold, M. L., & Kunte, K. K. (2017) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2017.05.007 · Cited by 128 · see citing works
Why Concatenation Fails Near the Anomaly Zone
Mendes, F. K., & Hahn, M. W. (2017) · Systematic Biology · doi:10.1093/sysbio/syx063 · Cited by 122 · see citing works
Self-citationDistinguishing Among Modes of Convergent Adaptation Using Population Genomic Data
Lee, K. M., & Coop, G. (2017) · Genetics · doi:10.1534/genetics.117.300417 · Cited by 121 · see citing works
Phylogenomics of the genusPopulusreveals extensive interspecific gene flow and balancing selection
Wang, M., Zhang, L., Zhang, Z., Li, M., Wang, D., Zhang, X., Xi, Z., Keefover‐Ring, K., Smart, L. B., DiFazio, S. P., et al. (2019) · New Phytologist · doi:10.1111/nph.16215 · Cited by 116 · see citing works
Extensive gene tree discordance and hemiplasy shaped the genomes of North American columnar cacti
Copetti, D., Búrquez, A., Bustamante, E., Charboneau, J. L. M., Childs, K. L., Eguiarte, L. E., Lee, S., Liu, T. L., McMahon, M. M., Whiteman, N. K., et al. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1706367114 · Cited by 114 · see citing works
Martin, C. H., & Richards, E. J. (2019) · Annual Review of Ecology Evolution and Systematics · doi:10.1146/annurev-ecolsys-110617-062443 · Cited by 110 · see citing works
Ghost Lineages Highly Influence the Interpretation of Introgression Tests
Tricou, T., Tannier, É., & de Vienne, D. M. (2022) · Systematic Biology · doi:10.1093/sysbio/syac011 · Cited by 110 · see citing works
Pervasive hybridizations in the history of wheat relatives
Glémin, S., Scornavacca, C., Dainat, J., Burgarella, C., Viader, V., Ardisson, M., Sarah, G., Santoni, S., David, J., & Ranwez, V. (2019) · Science Advances · doi:10.1126/sciadv.aav9188 · Cited by 109 · see citing works
Walker, J. F., Yang, Y. J., Feng, T., Timoneda, A., Mikenas, J. D., Hutchison, V., Edwards, C., Wang, N., Ahluwalia, S., Olivieri, J. E., et al. (2018) · American Journal of Botany · doi:10.1002/ajb2.1069 · Cited by 108 · see citing works
Long-term balancing selection drives evolution of immunity genes in Capsella
Koenig, D., Hagmann, J., Li, R., Bemm, F., Slotte, T., Neuffer, B., Wright, S., & Weigel, D. (2019) · eLife · doi:10.7554/elife.43606 · Cited by 108 · see citing works
Widespread adaptive evolution during repeated evolutionary radiations in New World lupins
Nevado, B., Atchison, G. W., Hughes, C. E., & Filatov, D. A. (2016) · Nature Communications · doi:10.1038/ncomms12384 · Cited by 106 · see citing works
Sun, C., Huang, J., Wang, Y., Zhao, X., Su, L., Thomas, G. W. C., Zhao, M., Zhang, X., Jungreis, I., Kellis, M., et al. (2020) · Molecular Biology and Evolution · doi:10.1093/molbev/msaa240 · Cited by 103 · see citing works
Self-citationSelective sorting of ancestral introgression in maize and teosinte along an elevational cline
Calfee, E., Gates, D. J., Lorant, A., Perkins, M. T., Coop, G., & Ross‐Ibarra, J. (2021) · PLoS Genetics · doi:10.1371/journal.pgen.1009810 · Cited by 101 · see citing works
A Guide to Genome‐Wide Association Mapping in Plants
Burghardt, L. T., Young, N. D., & Tiffin, P. (2017) · Current Protocols in Plant Biology · doi:10.1002/cppb.20041 · Cited by 100 · see citing works
Richards, E. J., & Martin, C. H. (2017) · PLoS Genetics · doi:10.1371/journal.pgen.1006919 · Cited by 99 · see citing works
Phylogenomic discordance suggests polytomies along the backbone of the large genus Solanum
Gagnon, E., Hilgenhof, R., Orejuela, A., McDonnell, A., Sablok, G., Aubriot, X., Giacomin, L. L., Gouvêa, Y., Bragionis, T., Stehmann, J. R., et al. (2022) · American Journal of Botany · doi:10.1002/ajb2.1827 · Cited by 97 · see citing works
Brandrud, M. K., Baar, J., Lorenzo, M. T., Athanasiadis, A., Bateman, R. M., Chase, M. W., Hedrén, M., & Paun, O. (2019) · Systematic Biology · doi:10.1093/sysbio/syz035 · Cited by 95 · see citing works
Primate phylogenomics uncovers multiple rapid radiations and ancient interspecific introgression
Vanderpool, D., Minh, B. Q., Lanfear, R., Hughes, D., Murali, S. C., Harris, R. A., Raveendran, M., Muzny, D. M., Hibbins, M. S., Williamson, R. J., et al. (2020) · PLoS Biology · doi:10.1371/journal.pbio.3000954 · Cited by 94 · see citing works
Self-citationAnalyzing Contentious Relationships and Outlier Genes in Phylogenomics
Walker, J. F., Brown, J. W., & Smith, S. A. (2018) · Systematic Biology · doi:10.1093/sysbio/syy043 · Cited by 93 · see citing works
Liu, Y., Li, D., Zhang, Q., Song, C., Zhong, C., Zhang, X., Wang, Y., Yao, X., Wang, Z., Zeng, S., et al. (2017) · New Phytologist · doi:10.1111/nph.14607 · Cited by 91 · see citing works
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) · Plant Communications · doi:10.1016/j.xplc.2023.100599 · Cited by 84 · see citing works
“This is illustrated by analyses of the wild tomato clade (Solanum section Lycopersicon), in which ancestral standing variation, introgression, and new mutations have contributed approximately equally to this recent adaptive radiation (Pease et al., 2016).”
Life in Deserts: The Genetic Basis of Mammalian Desert Adaptation
Rocha, J. L., Godinho, R., Brito, J. C., & Nielsen, R. (2021) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2021.03.007 · Cited by 83 · see citing works
The Meaning and Measure of Concordance Factors in Phylogenomics
Lanfear, R., & Hahn, M. W. (2024) · Molecular Biology and Evolution · doi:10.1093/molbev/msae214 · Cited by 82 · see citing works
Self-citationAdvances in Computational Methods for Phylogenetic Networks in the Presence of Hybridization
Elworth, R. A. L., Ogilvie, H. A., Zhu, J., & Nakhleh, L. K. (2019) · Computational biology · doi:10.1007/978-3-030-10837-3_13 · Cited by 81 · see citing works
Wu, M., Kostyun, J. L., Hahn, M. W., & Moyle, L. C. (2018) · Molecular Ecology · doi:10.1111/mec.14780 · Cited by 78 · see citing works
Self-citationHu, H., Hu, Q., Al-Shehbaz, I. A., Luo, X., Zeng, T., Guo, X., & Liu, J. (2016) · Frontiers in Plant Science · doi:10.3389/fpls.2016.01826 · Cited by 77 · see citing works
Plant speciation in the Quaternary
Kadereit, J. W., & Abbott, R. J. (2021) · Plant Ecology & Diversity · doi:10.1080/17550874.2021.2012849 · Cited by 77 · see citing works
Three new genome assemblies support a rapid radiation in Musa acuminata (wild banana)
Rouard, M., Droc, G., Martin, G., Sardos, J., Hueber, Y., Guignon, V., Cenci, A., Geigle, B., Hibbins, M. S., Yahiaoui, N., et al. (2018) · Genome Biology and Evolution · doi:10.1093/gbe/evy227 · Cited by 75 · see citing works
Self-citationYardeni, G., Viruel, J., Paris, M., Hess, J., Crego, C. G., Harpe, M. D. L., Rivera, N., Barfuss, M. H. J., Till, W., Guzmán‐Jacob, V., et al. (2021) · Molecular Ecology Resources · doi:10.1111/1755-0998.13523 · Cited by 75 · see citing works
Richards, E. J., Brown, J. M., Barley, A. J., Chong, R. A., & Thomson, R. C. (2018) · Systematic Biology · doi:10.1093/sysbio/syy013 · Cited by 74 · see citing works
Ranil, R. H. G., Prohens, J., Aubriot, X., Niran, H. M. L., Plazas, M., Fonseka, R. M., Vilanova, S., Fonseka, H. H. D., Gramazio, P., & Knapp, S. (2016) · Genetic Resources and Crop Evolution · doi:10.1007/s10722-016-0467-z · Cited by 73 · see citing works
Züst, T., Strickler, S. R., Powell, A. F., Mabry, M. E., An, H., Mirzaei, M., York, T., Holland, C. K., Kumar, P., Erb, M., et al. (2020) · eLife · doi:10.7554/elife.51712 · Cited by 73 · see citing works
Mehmood, F., Abdullah, A., Ubaid, Z., Shahzadi, I., Ahmed, I., Waheed, M. T., Poczai, P., & Mirza, B. (2020) · PeerJ · doi:10.7717/peerj.9552 · Cited by 72 · see citing works
Introgression among North American wild grapes (Vitis) fuels biotic and abiotic adaptation
Morales‐Cruz, A., Aguirre‐Liguori, J. A., Zhou, Y., Minio, A., Riaz, S., Walker, A. M., Cantù, D., & Gaut, B. S. (2021) · Genome biology · doi:10.1186/s13059-021-02467-z · Cited by 70 · see citing works
Understanding natural selection and similarity: Convergent, parallel and repeated evolution
Cerca, J. (2023) · Molecular Ecology · doi:10.1111/mec.17132 · Cited by 70 · see citing works
Modern Phylogenomics: Building Phylogenetic Trees Using the Multispecies Coalescent Model
Liu, L., Anderson, C. N. K., Pearl, D. K., & Edwards, S. V. (2019) · Methods in molecular biology · doi:10.1007/978-1-4939-9074-0_7 · Cited by 68 · see citing works
Quantifying the risk of hemiplasy in phylogenetic inference
Guerrero, R. F., & Hahn, M. W. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1811268115 · Cited by 68 · see citing works
Self-citationThe genetics of evolutionary radiations
Naciri, Y., & Linder, H. P. (2020) · Biological reviews/Biological reviews of the Cambridge Philosophical Society · doi:10.1111/brv.12598 · Cited by 67 · see citing works
Olave, M., & Meyer, A. (2020) · Systematic Biology · doi:10.1093/sysbio/syaa005 · Cited by 66 · see citing works
Assessing biological factors affecting postspeciation introgression
Hamlin, J. A. P., Hibbins, M. S., & Moyle, L. C. (2020) · Evolution Letters · doi:10.1002/evl3.159 · Cited by 66 · see citing works
Self-citationGene Tree Discordance Can Generate Patterns of Diminishing Convergence over Time
Mendes, F. K., Hahn, Y., & Hahn, M. W. (2016) · Molecular Biology and Evolution · doi:10.1093/molbev/msw197 · Cited by 66 · see citing works
Self-citationWalker, J. F., Yang, Y. J., Moore, M. J., Mikenas, J. D., Timoneda, A., Brockington, S. F., & Smith, S. A. (2017) · American Journal of Botany · doi:10.3732/ajb.1700083 · Cited by 65 · see citing works
Liu, S., Zhang, L., Sang, Y., Lai, Q., Zhang, X., Jia, C., Long, Z., Wu, J., Ma, T., Mao, K., et al. (2022) · Molecular Biology and Evolution · doi:10.1093/molbev/msac008 · Cited by 65 · see citing works
Phylogenomic conflict coincides with rapid morphological innovation
Parins‐Fukuchi, C., Stull, G. W., & Smith, S. A. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2023058118 · Cited by 64 · see citing works
Kiefer, C., Willing, E., Jiao, W., Sun, H., Piednoël, M., Hümann, U., Hartwig, B., Koch, М. A., & Schneeberger, K. (2019) · Nature Plants · doi:10.1038/s41477-019-0486-9 · Cited by 64 · see citing works
Intercontinental genomic parallelism in multiple three-spined stickleback adaptive radiations
Magalhaes, I. S., Whiting, J. R., D’Agostino, D., Hohenlohe, P. A., Mahmud, M., Bell, M. A., Skúlason, S., & MacColl, A. D. C. (2020) · Nature Ecology & Evolution · doi:10.1038/s41559-020-01341-8 · Cited by 64 · see citing works
Weston, D. J., Turetsky, M. R., Johnson, M. G., Granath, G., Lindo, Z., Belyea, L. R., Rice, S. K., Hanson, D. T., Engelhardt, K. A. M., Schmutz, J., et al. (2017) · New Phytologist · doi:10.1111/nph.14860 · Cited by 63 · see citing works
Lopes, F., de Oliveira, L. R., Kessler, A., Beux, Y., Crespo, E. A., Cárdenas‐Alayza, S., Majluf, P., Sepúlveda, M., Brownell, R. L., Franco‐Trecu, V., et al. (2020) · Systematic Biology · doi:10.1093/sysbio/syaa099 · Cited by 62 · see citing works
Fan, P., Miller, A. M., Liu, X., Jones, A. D., & Last, R. L. (2017) · Nature Communications · doi:10.1038/s41467-017-02045-7 · Cited by 62 · see citing works
Dowell, N. L., Giorgianni, M. W., Griffin, S., Kassner, V. A., Selegue, J. E., Sanchez, E. E., & Carroll, S. B. (2018) · Current Biology · doi:10.1016/j.cub.2018.02.031 · Cited by 60 · see citing works
The case for the continued use of the genus name Mimulus for all monkeyflowers
Lowry, D. B., Sobel, J. M., Angert, A. L., Ashman, T., Baker, R. L., Blackman, B. K., Brandvain, Y. J., Byers, K. J. R. P., Cooley, A. M., Coughlan, J. M., et al. (2019) · Taxon · doi:10.1002/tax.12122 · Cited by 60 · see citing works
Choi, J. Y., Dai, X., Alam, O., Peng, J. Z., Rughani, P., Hickey, S., Harrington, E., Juul, S., Ayroles, J. F., Purugganan, M. D., et al. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2023801118 · Cited by 58 · see citing works
Conserved Nonexonic Elements: A Novel Class of Marker for Phylogenomics
Edwards, S. V., Cloutier, A., & Baker, A. J. (2017) · Systematic Biology · doi:10.1093/sysbio/syx058 · Cited by 57 · see citing works
Fukushima, K., & Pollock, D. D. (2023) · Nature Ecology & Evolution · doi:10.1038/s41559-022-01932-7 · Cited by 55 · see citing works
Zhang, W., Zhang, X., Li, K., Wang, C., Cai, L., Zhuang, W.-Y., Xiang, M., & Liu, X. (2018) · Mycology: An International Journal on Fungal Biology · doi:10.1080/21501203.2018.1478333 · Cited by 54 · see citing works
Polyploidy breaks speciation barriers in Australian burrowing frogs Neobatrachus
Novikova, P. Y., Brennan, I. G., Booker, W. W., Mahony, M. J., Doughty, P., Lemmon, A. R., Lemmon, E. M., Roberts, J. D., Yant, L. J., de Peer, Y. V., et al. (2020) · PLoS Genetics · doi:10.1371/journal.pgen.1008769 · Cited by 53 · see citing works
The Next Generation of Adaptive Radiation Studies in Plants
Schenk, J. J. (2021) · International Journal of Plant Sciences · doi:10.1086/713445 · Cited by 53 · see citing works
Phuong, M. A., & Mahardika, G. N. (2018) · Molecular Biology and Evolution · doi:10.1093/molbev/msy034 · Cited by 53 · see citing works
Lamichhaney, S., Card, D. C., Grayson, P., Tonini, J. F. R., Bravo, G. A., Näpflin, K., Termignoni‐García, F., Torres, C. R., Burbrink, F. T., Clarke, J. A., et al. (2019) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2018.0248 · Cited by 53 · see citing works
AGOUTI: improving genome assembly and annotation using transcriptome data
Zhang, S. V., Zhuo, L., & Hahn, M. W. (2016) · GigaScience · doi:10.1186/s13742-016-0136-3 · Cited by 52 · see citing works
Self-citationFerrero, V., Baeten, L., Blanco‐Sánchez, L., Planelló, R., Díaz‐Pendón, J. A., Rodríguez‐Echeverría, S., Haegeman, A., & de la Peña, E. (2019) · New Phytologist · doi:10.1111/nph.16353 · Cited by 50 · see citing works
Ahammad, K., Ieda, R., Hosoya, S., Fujikawa, D., Atsumi, K., Tajima, S., Nozawa, A., Koyama, T., Hirase, S., Nakamura, O., et al. (2022) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2121469119 · Cited by 50 · see citing works
A multispecies coalescent model for quantitative traits
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Self-citationAubriot, X., Knapp, S., Syfert, M. M., Poczai, P., & Buerki, S. (2018) · American Journal of Botany · doi:10.1002/ajb2.1133 · Cited by 49 · see citing works
Evaluating UCE Data Adequacy and Integrating Uncertainty in a Comprehensive Phylogeny of Ants
Borowiec, M. L., Zhang, Y. M., Neves, K., Ramalho, M. O., Fisher, B. L., Lucky, A., & Moreau, C. S. (2025) · Systematic Biology · doi:10.1093/sysbio/syaf001 · Cited by 48 · see citing works
Weak coordination between leaf structure and function among closely related tomato species
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The dynamics of introgression across an avian radiation
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Medina, R., Johnson, M. G., Liu, Y., Wilding, N., Hedderson, T. A. J., Wickett, N. J., & Goffinet, B. (2017) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2017.12.002 · Cited by 47 · see citing works
- Authors
- Pease, J. B., Haak, D. C., Hahn, M. W., & Moyle, L. C.
- Affiliations
- Indiana University Bloomington (US)
- Corresponding author
- Moyle, Leonie C.
- Venue
- PLOS Biology
- Publisher
- Public Library of Science (PLoS)
- Published
- 2016-02-12
- Volume
- 14
- Issue
- 2
- Pages
- e1002379
- ISSN
- 1544-9173 (ISSN-L)
- 1545-7885
- PMC
- PMC4752443
- OpenAlex
- W2272393905
- Cited by
- 432
- References
- 104
- Citations by year
- 2026: 34 · 2025: 37 · 2024: 37 · 2023: 40 · 2022: 36 · 2021: 50 · 2020: 45 · 2019: 50 · 2018: 43 · 2017: 36 · 2016: 22 · 2015: 1
- FWCI
- 58.95
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- PLoS Biology (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Figshare (submittedVersion, cc-by)
- VTechWorks (Virginia Tech) (submittedVersion, cc-by)
- Funders
- National Science Foundation (1136707)
- Division of Environmental Biology (1136707)
- Topics
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Life Sciences › Agricultural and Biological Sciences › Ecology, Evolution, Behavior and Systematics › Plant Diversity and Evolution
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- species radiation, speciation, adaptive genetic variation, introgression, de novo gene evolution, phylogenetic incongruence, whole transcriptome, diversification
- MeSH terms
- Polymorphism, Genetic, Solanum lycopersicum, Genomics, Genetic Speciation
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