Phylogenomics reveals three sources of adaptive variation during a rapid radiation

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1. Impacts of Inference Method and Data set Filtering on Phylogenomic Resolution in a Rapid Radiation of Ground Squirrels (Xerinae: Marmotini)
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2. Targeted Enrichment of Large Gene Families for Phylogenetic Inference: Phylogeny and Molecular Evolution of Photosynthesis Genes in the Portullugo Clade (Caryophyllales)
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3. Target sequence capture in orchids: Developing a kit to sequence hundreds of single‐copy loci
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4. Incidence and developmental timing of endosperm failure in post-zygotic isolation between wild tomato lineages
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5. Trans‐lineage polymorphism and nonbifurcating diversification of the genus Picea
   Shuo Feng, Dafu Ru, Yongshuai Sun, Kangshan Mao, RICHARD IAN MILNE, Jianquan Liu · 2018 · New Phytologist
6. Adaptive Evolution Is Common in Rapid Evolutionary Radiations
   Bruno Nevado, Edgar L. Y. Wong, Owen G. Osborne, Dmitry A. Filatov · 2019 · Current Biology
7. The de Novo Reference Genome and Transcriptome Assemblies of the Wild Tomato Species Solanum chilense Highlights Birth and Death of NLR Genes Between Tomato Species
   Remco Stam, Tetyana Nosenko, Anja C. Hörger, Wolfgang Stephan, Michael A. Seidel, José Manuel Monroy Kuhn, Georg Haberer, Aurélien Tellier · 2019 · G3 Genes Genomes Genetics
8. The Central Role of Taxonomy in the Study of Neotropical Biodiversity
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9. The genomic revolution and species delimitation in birds (and other organisms): Why phenotypes should not be overlooked
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10. Interspecific reproductive barriers between sympatric populations of wild tomato species (Solanum section Lycopersicon)
    You Soon Baek, Suzanne M. Royer, Amanda K. Broz, Paul A. Covey, Gloria López‐Casado, Reynaldo Nuñez, Philip James Kear, Merideth Bonierbale, Matilde Orrillo, Esther van der Knaap et al. · 2016 · American Journal of Botany
11. Mating system transitions in Solanum habrochaites impact interactions between populations and species
    Amanda K. Broz, April M. Randle, Shelley A. Sianta, Alejandro Tovar‐Méndez, Bruce McClure, Patricia A. Bedinger · 2016 · New Phytologist
12. Seeing through the hedge: Phylogenomics of Thuja (Cupressaceae) reveals prominent incomplete lineage sorting and ancient introgression for Tertiary relict flora
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13. Genomic Signatures of Reinforcement
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14. Complex patterns of hybridization and introgression across evolutionary timescales in Mexican whiptail lizards (Aspidoscelis)
    Anthony J. Barley, Adrián Nieto‐Montes de, Tod W. Reeder, Norma L. Manríquez‐Morán, José Carlos Arenas Monroy, Oswaldo Hernández‐Gallegos, Robert C. Thomson · 2018 · Molecular Phylogenetics and Evolution
15. Impact of homologous recombination on core genome phylogenies
    Caroline M. Stott, Louis‐Marie Bobay · 2020 · BMC Genomics
16. A highly resolved nuclear phylogeny uncovers strong phylogenetic conservatism and correlated evolution of fruit color and size in Solanum L.
    João Vitor S. Messeder, Tomás A. Carlo, Guojin Zhang, Juan David Tovar Duran, César Arana, Jie Huang, Chien‐Hsun Huang, Hong Mā · 2024 · New Phytologist
17. Genome-Guided Phylo-Transcriptomic Methods and the Nuclear Phylogenetic Tree of the Paniceae Grasses
    Jacob D. Washburn, James C. Schnable, Gavin C. Conant, Thomas P. Brutnell, Ying Shao, Yang Zhang, Martha L Ludwig, Gerrit Davidse, J. Chris Pires · 2017 · Scientific Reports
18. Novel phylogenetic methods are needed for understanding gene function in the era of mega-scale genome sequencing
    László G. Nagy, Zsolt Merényi, Botond Hegedüs, Balázs Bálint · 2019 · Nucleic Acids Research
19. Enhanced pollen tube performance at high temperature contributes to thermotolerant fruit and seed production in tomato
    Sorel V Yimga Ouonkap, P Meenakshisundaram, Kelsey Pryze, Emma Jong, Mohammad Foteh Ali, Benjamin S. Styler, Rasha Althiab Almasaud, Alexandria F. Harkey, Robert W. Reid, Ann E. Loraine et al. · 2024 · Current Biology
20. Reinforcement and the Proliferation of Species
    Gina M. Calabrese, Karin S. Pfennig · 2019 · Journal of Heredity
21. The Role of Introgression During the Radiation of Endemic Fishes Adapted to Living at Extreme Altitudes in the Tibetan Plateau
    Yuting Qian, Minghui Meng, Chaowei Zhou, Haiping Liu, Haifeng Jiang, Youwei Xu, Wenjun Chen, Zufa Ding, Yang Liu, Xiong Gong et al. · 2023 · Molecular Biology and Evolution
22. Standing geographic variation in eclosion time and the genomics of host race formation inRhagoletis pomonellafruit flies
    Meredith M. Doellman, Scott Patrick Egan, Gregory J. Ragland, Peter J. Meyers, Glen R. Hood, Thomas H. Q. Powell, Peter Lazorchak, Daniel A. Hahn, Stewart H. Berlocher, Patrik Nosil et al. · 2018 · Ecology and Evolution
23. Natural genetic variation in dynamic photosynthesis is correlated with stomatal anatomical traits in diverse tomato species across geographical habitats
    Yugo Yoshiyama, Yu Wakabayashi, Kristin L. Mercer, Saneyuki Kawabata, T. Kobayashi, Toshihito Tabuchi, Wataru Yamori · 2024 · Journal of Experimental Botany
24. HT proteins contribute to S‐ RN ase‐independent pollen rejection in Solanum
    Alejandro Tovar‐Méndez, Lu Lu, Bruce McClure · 2016 · The Plant Journal
25. Determining the probability of hemiplasy in the presence of incomplete lineage sorting and introgression
    Mark S. Hibbins, Matthew J. S. Gibson, Matthew W. Hahn · 2020 · eLife
26. The perils of intralocus recombination for inferences of molecular convergence
    Fábio K. Mendes, Andrew P. Livera, Matthew W. Hahn · 2019 · Philosophical Transactions of the Royal Society B Biological Sciences
27. Molecular mechanisms of postmating prezygotic reproductive isolation uncovered by transcriptome analysis
    James B. Pease, Rafael F. Guerrero, Natasha A. Sherman, Matthew W. Hahn, Leonie C. Moyle · 2016 · Molecular Ecology
28. Differential gene expression during early development in recently evolved and sympatric Arctic charr morphs
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29. Hybridization drives genetic erosion in sympatric desert fishes of western North America
    Tyler K. Chafin, Marlis R. Douglas, Bradley T. Martin, Michael Edward Douglas · 2019 · Heredity
30. A new eIF4E1 allele characterized by RNAseq data mining is associated with resistance to potato virus Y in tomato albeit with a low durability
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31. Divergent selection and primary gene flow shape incipient speciation of a riparian tree on Hawaii island
    Choi, Jae Young, Purugganan, Michael, Stacy, Elizabeth A · 2020 · Molecular Biology and Evolution
32. Reconsidering cytonuclear discordance in the genomic age
    Drew A. Larson, Michael W. Itgen, Robert D. Denton, Matthew W. Hahn · 2025 · Evolution
33. Adaptive Genetic Divergence Despite Significant Isolation-by-Distance in Populations of Taiwan Cow-Tail Fir (Keteleeria davidiana var. formosana)
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34. Hybrids and horizontal transfer: introgression allows adaptive allele discovery
    Roswitha Schmickl, Sarah Marburger, Sian Bray, Levi J Yant · 2017 · Journal of Experimental Botany
35. A Phylogenomic Analysis of the Floral Transcriptomes of Sexually Deceptive and Rewarding European Orchids, Ophrys and Gymnadenia
    Laura Piñeiro Fernández, Kelsey J.R.P. Byers, Jing Cai, Khalid E. M. Sedeek, Roman T. Kellenberger, Alessia Russo, Weihong Qi, Catharine Aquino, Philipp M. Schlüter · 2019 · Frontiers in Plant Science
36. Genome-wide patterns of regulatory divergence revealed by introgression lines
    Rafael F. Guerrero, Matthew W. Hahn, Leonie C. Moyle, Amanda L. Posto · 2016 · Evolution
37. Ultraconserved Elements Improve the Resolution of Difficult Nodes within the Rapid Radiation of Neotropical Sigmodontine Rodents (Cricetidae: Sigmodontinae)
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38. Wild tomato endosperm transcriptomes reveal common roles of genomic imprinting in both nuclear and cellular endosperm
    Morgane Roth, Ana Marcela Florez‐Rueda, Margot Paris, Thomas Städler · 2018 · The Plant Journal
39. Admixture may be extensive among hyperdominant Amazon rainforest tree species
    Drew A. Larson, Oscar M. Vargas, Alberto Vicentini, Christopher W. Dick · 2021 · New Phytologist
40. Phylogenomic comparative methods: Accurate evolutionary inferences in the presence of gene tree discordance
    Mark S. Hibbins, Lara C. Breithaupt, Matthew W. Hahn · 2023 · Proceedings of the National Academy of Sciences
41. Dispersal is associated with morphological innovation, but not increased diversification, inCyphostemma(Vitaceae)
    David J. Hearn, Margaret E. K. Evans, Ben Wolf, Michael McGinty, Jun Wen · 2018 · Journal of Systematics and Evolution
42. Introgression lines of Solanum sitiens, a wild nightshade of the Atacama Desert, in the genome of cultivated tomato
    Roger T. Chetelat, Xiaoqiong Qin, Meilian Tan, Diana Burkart‐Waco, Yosuke Moritama, Xiuwen Huo, Tim Wills, Ricardo A. Pertuzé · 2019 · The Plant Journal
43. Recombination Variation Shapes Phylogeny and Introgression in Wild Diploid Strawberries
    Chao Feng, Jing Wang, Aaron Liston, Ming Kang · 2023 · Molecular Biology and Evolution
44. Reticulate evolution within a spruce ( Picea ) species complex revealed by population genomic analysis
    Yongshuai Sun, Richard J. Abbott, Zhiqiang Lu, Kangshan Mao, Lei Zhang, Xiaojuan Wang, Dafu Ru, Jianquan Liu · 2018 · Evolution
45. Rampant chloroplast capture in Sarracenia revealed by plastome phylogeny
    Ethan A. Baldwin, Mason C. McNair, Jim Leebens‐Mack · 2023 · Frontiers in Plant Science
46. Population Genomics in Wild Tomatoes—The Interplay of Divergence and Admixture
    Ian Beddows, A. K. Reddy, Thorsten Kloesges, Laura E Rose · 2017 · Genome Biology and Evolution
47. Phylotranscriptomic Insights into the Diversification of EndothermicThunnusTunas
    Adam Ciezarek, Owen G. Osborne, Oliver N. Shipley, Edward J. Brooks, S Tracey, Jaime McAllister, Luke D. Gardner, Michael J.E. Sternberg, Barbara A. Block, Vincent Savolainen · 2018 · Molecular Biology and Evolution
48. The Tomato Interspecific NB-LRR Gene Arsenal and Its Impact on Breeding Strategies
    Giuseppe Andolfo, Nunzio D’Agostino, Luigi Frusciante, Maria Raffaella Ercolano · 2021 · Genes
49. Artifactual Orthologs and the Need for Diligent Data Exploration in Complex Phylogenomic Datasets: A Museomic Case Study from the Andean Flora
    Laura A. Frost, Ana M. Bedoya, Laura P. Lagomarsino · 2024 · Systematic Biology
50. Extensive genetic differentiation between recently evolved sympatric Arctic charr morphs
    Jóhannes Guðbrandsson, Kalina Hristova Kapralova, Sigríður Rut Franzdóttir, Þóra Margrét Bergsveinsdóttir, Völundur Hafstað, Zophonías Oddur Jónsson, Sigurður Sveinn Snorrason, Arnar Pálsson · 2019 · Ecology and Evolution
51. Drainage-structuring of ancestral variation and a common functional pathway shape limited genomic convergence in natural high- and low-predation guppies
    James R. Whiting, Josephine R. Paris, Mijke J. van der Zee, Paul J. Parsons, Detlef Weigel, Bonnie A. Fraser · 2021 · PLoS Genetics
52. Pervasive Introgression During Rapid Diversification of the European Mountain Genus Soldanella (L.) (Primulaceae)
    Marek Slovák, Andrea Melichárková, Eliška Gbúrová Štubňová, Jaromír Kučera, Terezie M. Mandáková, Jan Smyčka, Sébastien Lavergne, NICODEMO GIUSEPPE PASSALACQUA, Peter Vďačný, Ovidiu Paun · 2022 · Systematic Biology
53. Genome Evolution and the Future of Phylogenomics of Non-Avian Reptiles
    Daren C. Card, W. Bryan Jennings, Scott V. Edwards · 2023 · Animals
54. Phylogenomics reveal extensive phylogenetic discordance due to incomplete lineage sorting following the rapid radiation of alpine butterflies (Papilionidae: Parnassius )
    Bo He, Youjie Zhao, Chengyong Su, Gonghua Lin, Yunliang Wang, Luyan Li, Junye Ma, Qun Yang, Jiasheng Hao · 2023 · Systematic Entomology
55. Layered evolution of gene expression in “superfast” muscles for courtship
    James B. Pease, Robert J. Driver, David A. de la Cerda, Lainy B. Day, Willow R. Lindsay, Barney A. Schlinger, Eric R. Schuppe, Christopher N. Balakrishnan, Matthew J. Fuxjager · 2022 · Proceedings of the National Academy of Sciences
56. Venom Gene Sequence Diversity and Expression Jointly Shape Diet Adaptation in Pitvipers
    Andrew J. Mason, Matthew L. Holding, Rhett M. Rautsaw, Darin R. Rokyta, Christopher L. Parkinson, H. Lisle Gibbs · 2022 · Molecular Biology and Evolution
57. Hybridization alters the shape of the genotypic fitness landscape, increasing access to novel fitness peaks during adaptive radiation
    Austin H. Patton, Emilie J. Richards, Katelyn J. Gould, Logan K. Buie, Christopher H. Martin · 2022 · eLife
58. Chromosome-scale genome assemblies of wild tomato relatives Solanum habrochaites and Solanum galapagense reveal structural variants associated with stress tolerance and terpene biosynthesis
    Xiaofen Yu, Minghao Qu, Yanna Shi, Chenlu Hao, Sumin Guo, Zhangjun Fei, Lei Gao · 2022 · Horticulture Research
59. Furcation and fusion: The phylogenetics of evolutionary novelty
    Todd H. Oakley · 2017 · Developmental Biology
60. Genome Sequence of Jaltomata Addresses Rapid Reproductive Trait Evolution and Enhances Comparative Genomics in the Hyper-Diverse Solanaceae
    Meng Wu, Jamie L. Kostyun, Leonie C. Moyle · 2019 · Genome Biology and Evolution
61. Genomic footprints of repeated evolution of CAM photosynthesis in a Neotropical species radiation
    Marylaure de La Harpe, Margot Paris, Jaqueline Hess, Michael H. J. Barfuss, Martha L. Serrano‐Serrano, Arindam Ghatak, Palak Chaturvedi, Wolfram Weckwerth, Walter Till, Nicolas Salamin et al. · 2020 · Plant Cell & Environment
62. Recent Perspective of Next Generation Sequencing: Applications in Molecular Plant Biology and Crop Improvement
    Prashant Yadav, Era Vaidya Malhotra, Reema Rani, Navneet Kumar Yadav, Bhupender Singh, P. K. Rai, Dhiraj Singh · 2016 · Proceedings of the National Academy of Sciences India Section B Biological Sciences
63. Fast Bayesian Inference of Phylogenies from Multiple Continuous Characters
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64. Detecting introgression despite phylogenetic uncertainty: The case of the South American siskins
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65. Small‐spored Alternaria spp. (section Alternaria ) are common pathogens on wild tomato species
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66. Resolving Marine–Freshwater Transitions by Diatoms Through a Fog of Gene Tree Discordance
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67. PhyloAcc-GT: A Bayesian Method for Inferring Patterns of Substitution Rate Shifts on Targeted Lineages Accounting for Gene Tree Discordance
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68. Toward the integration of speciation research
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69. Mutations in two pollen self‐incompatibility factors in geographically marginal populations of Solanum habrochaites impact mating system transitions and reproductive isolation
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70. Integrating Sequence Capture and Restriction Site-Associated DNA Sequencing to Resolve Recent Radiations of Pelagic Seabirds
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71. Population Genomics of Adaptive Radiation
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72. Heterogeneity of a dwarf phenotype in Dutch traditional chicken breeds revealed by genomic analyses
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73. The genetic architecture and evolution of life-history divergence among perennials in the Mimulus guttatus species complex
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74. Climatic Diversity and Ecological Descriptors of Wild Tomato Species (Solanum sect. Lycopersicon) and Close Related Species (Solanum sect. Juglandifolia y sect. Lycopersicoides) in Latin America
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75. How to Validate a Bayesian Evolutionary Model
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76. Greatly reduced phylogenetic structure in the cultivated potato clade (Solanum section Petota pro parte)
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77. Incomplete lineage sorting and ancient admixture, and speciation without morphological change in ghost-worm cryptic species
    José Cerca, Angel G. Rivera‐Colón, Mafalda S. Ferreira, Mark Ravinet, Michael D. Nowak, Julian Catchen, Torsten H. Struck · 2021 · PeerJ
78. Widespread selection and gene flow shape the genomic landscape during a radiation of monkeyflowers
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79. Phylogenomics of mulberries (Morus, Moraceae) inferred from plastomes and single copy nuclear genes
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80. Deciphering salt stress responses in Solanum pimpinellifolium through high‐throughput phenotyping
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81. Using mustard genomes to explore the genetic basis of evolutionary change
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82. Species in the Age of Discordance
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83. Incomplete lineage sorting and long-branch attraction confound phylogenomic inference of Pancrustacea
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84. Situación taxonómica de las especies del género Polylepis. Implicancias para los estudios ecológicos, la conservación y la restauración de sus bosques
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85. Reproductive Proteins Evolve Faster Than Non-reproductive Proteins Among Solanum Species
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86. Mutational load and adaptive variation are shaped by climate and species range dynamics in Vitis arizonica
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87. Phylogenomics reveals the slow-burning fuse of diatom evolution
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88. Edaphoclimatic Descriptors of Wild Tomato Species (Solanum Sect. Lycopersicon) and Closely Related Species (Solanum Sect. Juglandifolia and Sect. Lycopersicoides) in South America
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89. The puzzle of plant hybridisation: a high propensity to hybridise but few hybrid zones reported
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90. Evolutionary radiation of the Eurasian Pinus species under pervasive gene flow
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91. TAI vacuolar invertase orthologs: the interspecific variability in tomato plants (Solanum section Lycopersicon)
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92. Evolutionary history of two pollen self‐incompatibility factors reveals alternate routes to self‐compatibility within Solanum
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93. Evolution of strong reproductive isolation in plants: broad-scale patterns and lessons from a perennial model group
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94. Migration through a Major Andean Ecogeographic Disruption as a Driver of Genetic and Phenotypic Diversity in a Wild Tomato Species
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95. Mutation rates in seeds and seed-banking influence substitution rates across the angiosperm phylogeny
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96. Structural variation underlies functional diversity at methyl salicylate loci in tomato
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97. CAGEE: Computational Analysis of Gene Expression Evolution
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98. Genomewide variation provides insight into evolutionary relationships in a monkeyflower species complex (Mimulus sect. Diplacus)
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99. What can be learned by scanning the genome for molecular convergence in wild populations?
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100. Evolution of putative barrier loci at an intermediate stage of speciation with gene flow in campions (Silene)
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