REFERENCES
Alber, A., & Ehlting, J. (2012). Cytochrome P450s in lignin biosynthesis. Advances in Botanical Research, 61 , 113-143.
Alber, A. V., Renault, H., Basilio‐Lopes, A., Bassard, J. E., Liu, Z., Ullmann, P., . . . Werck‐Reichhart, D. (2019). Evolution of coumaroyl conjugate 3‐hydroxylases in land plants: lignin biosynthesis and defense. The Plant Journal, 99 (5), 924-936.
Alexander, D. H., Novembre, J., & Lange, K. (2009). Fast model-based estimation of ancestry in unrelated individuals. Genome research, 19 (9), 1655-1664.
Anderson, J. T., & Song, B. H. (2020). Plant adaptation to climate change—Where are we? Journal of Systematics and Evolution, 58 (5), 533-545.
Andrew, S. (2010). A quality control tool for high throughput sequence data. Fast QC, 532 .
Ashikari, M., Sakakibara, H., Lin, S., Yamamoto, T., Takashi, T., Nishimura, A., . . . Matsuoka, M. (2005). Cytokinin oxidase regulates rice grain production. science, 309 (5735), 741-745.
Bailey, T. L., & Elkan, C. (1994). Fitting a mixture model by expectation maximization to discover motifs in bipolymers.
Ballerini, E. S., Kramer, E. M., & Hodges, S. A. (2019). Comparative transcriptomics of early petal development across four diverse species of Aquilegia reveal few genes consistently associated with nectar spur development. BMC Genomics, 20 (1), 668.
Baron, K. N., Schroeder, D. F., & Stasolla, C. (2012). Transcriptional response of abscisic acid (ABA) metabolism and transport to cold and heat stress applied at the reproductive stage of development in Arabidopsis thaliana. Plant Science, 188 , 48-59.
Bates, D., Mächler, M., Bolker, B., & Walker, S. (2014). Fitting linear mixed-effects models using lme4. arXiv preprint arXiv:1406.5823 .
Bolger, A. M., Lohse, M., & Usadel, B. (2014). Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics, 30 (15), 2114-2120.
Brothers, A. N., & Delph, L. F. (2017). Divergence in style length and pollen size leads to a postmating‐prezygotic reproductive barrier among populations of Silene latifolia. Evolution, 71 (6), 1532-1540.
Brousseau, L., Fine, P. V., Dreyer, E., Vendramin, G. G., & Scotti, I. (2021). Genomic and phenotypic divergence unveil microgeographic adaptation in the Amazonian hyperdominant tree Eperua falcataAubl.(Fabaceae). Molecular ecology, 30 (5), 1136-1154.
Browning, S. R., & Browning, B. L. (2007). Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. The American journal of human genetics, 81 (5), 1084-1097.
Cahill, A. E., Aiello‐Lammens, M. E., Caitlin Fisher‐Reid, M., Hua, X., Karanewsky, C. J., Ryu, H. Y., . . . Wiens, J. J. (2014). Causes of warm‐edge range limits: systematic review, proximate factors and implications for climate change. Journal of Biogeography, 41 (3), 429-442.
Celep, F., Atalay, Z., Dikmen, F., Doǧan, M., Sytsma, K. J., & Claßen-Bockhoff, R. (2020). Pollination ecology, specialization, and genetic isolation in sympatric bee-pollinated Salvia (Lamiaceae).International Journal of Plant Sciences, 181 (8), 800-811.
Chan, Z. (2012). Expression profiling of ABA pathway transcripts indicates crosstalk between abiotic and biotic stress responses in Arabidopsis. Genomics, 100 (2), 110-115.
Chen, C., Bai, Y., Fang, X., Guo, H., Meng, Q., Zhang, W., . . . Murodov, A. (2019). A Late Miocene Terrestrial Temperature History for the Northeastern Tibetan Plateau’s Period of Tectonic Expansion.Geophysical Research Letters, 46 (14), 8375-8386.
Cingolani, P., Platts, A., Wang, L. L., Coon, M., Nguyen, T., Wang, L., . . . Ruden, D. M. (2012). A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly, 6 (2), 80-92.
Coop, G., Witonsky, D., Di Rienzo, A., & Pritchard, J. K. (2010). Using environmental correlations to identify loci underlying local adaptation.Genetics, 185 (4), 1411-1423.
Coyne, J. A. (2016). Theodosius Dobzhansky on hybrid sterility and speciation. Genetics, 202 (1), 5-7.
Coyne, J. A., & Orr, H. A. (2004). Speciation (Vol. 37): Sinauer Associates Sunderland, MA.
Dai, W.-K., Amboka, G. M., Kadiori, E. L., Wang, Q.-F., & Yang, C.-F. (2017). Phenotypic plasticity of floral traits and pollination adaption in an alpine plant Pedicularis siphonantha D. Don when transplanted from higher to lower elevation in Eastern Himalaya.Journal of Mountain Science, 14 (10), 1995-2002.
Dalgleish, H. J., Koons, D. N., Hooten, M. B., Moffet, C. A., & Adler, P. B. (2011). Climate influences the demography of three dominant sagebrush steppe plants. Ecology, 92 (1), 75-85.
Danecek, P., Auton, A., Abecasis, G., Albers, C. A., Banks, E., DePristo, M. A., . . . Sherry, S. T. (2011). The variant call format and VCFtools. Bioinformatics, 27 (15), 2156-2158.
Darwin, C. (1859). The origin of species. Harvard classics. PF Collier & Son, New York , 1909-1914.
Des Marais, D. L., & Rausher, M. D. (2010). Parallel evolution at multiple levels in the origin of hummingbird pollinated flowers in Ipomoea. Evolution: International Journal of Organic Evolution, 64 (7), 2044-2054.
Dobin, A., Davis, C. A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., . . . Gingeras, T. R. (2013). STAR: ultrafast universal RNA-seq aligner. Bioinformatics, 29 (1), 15-21.
Dobzhansky, T. (1982). Genetics and the Origin of Species : Columbia university press.
Doyle, J. J., & Doyle, J. L. (1987). A rapid DNA isolation procedure for small quantities of fresh leaf tissue . Retrieved from
Edwards, M. B., Choi, G. P., Derieg, N. J., Min, Y., Diana, A. C., Hodges, S. A., . . . Ballerini, E. S. (2021). Genetic architecture of floral traits in bee-and hummingbird-pollinated sister species ofAquilegia (columbine). bioRxiv .
Erst, A., Shaulo, D., & Schmakov, A. (2013). Aquilegia kamelinii(Ranunculaceae)–a new species from North Asia. Turczaninowia, 16 (3), 8-10.
Erst, A. S., Pendry, C. A., Erst, T. V., Ikeda, H., Xiang, K., & Wang, W. (2020). Two new taxa and one new record of Aquilegia(Ranunculaceae) from India and Pakistan. Phytotaxa, 439 (2), 108-118.
Erst, A. S., Wang, W., Yu, S. X., Xiang, K., Wang, J., Shaulo, D. N., . . . Nobis, M. (2017). Two new species and four new records ofAquilegia (Ranunculaceae) from China. Phytotaxa, 316 (2), 121-137.
Farminhão, J. N., Verlynde, S., Kaymak, E., Droissart, V., Simo-Droissart, M., Collobert, G., . . . Stévart, T. (2021). Rapid radiation of angraecoids (Orchidaceae, Angraecinae) in tropical Africa characterised by multiple karyotypic shifts under major environmental instability. Molecular Phylogenetics and Evolution, 159 , 107105.
Feder, J. L., Opp, S. B., Wlazlo, B., Reynolds, K., Go, W., & Spisak, S. (1994). Host fidelity is an effective premating barrier between sympatric races of the apple maggot fly. Proceedings of the National Academy of Sciences, 91 (17), 7990-7994.
Fedoreyeva, L. I., Vanyushin, B. F., & Baranova, E. N. (2020). Peptide AEDL alters chromatin conformation via histone binding. AIMS Biophysics, 7 (1), 1-16.
Filiault, D. L., Ballerini, E. S., Mandakova, T., Aköz, G., Derieg, N. J., Schmutz, J., . . . Hayes, R. D. (2018). The Aquilegia genome provides insight into adaptive radiation and reveals an extraordinarily polymorphic chromosome with a unique history. Elife, 7 , e36426.
Foll, M., & Gaggiotti, O. (2008). A genome-scan method to identify selected loci appropriate for both dominant and codominant markers: a Bayesian perspective. Genetics, 180 (2), 977-993.
Futuyma, D. J. (1998). Evolutionary biology. In: Sinauer Associates, Sunderland, MA.
George, J. P., Schueler, S., Grabner, M., Karanitsch‐Ackerl, S., Mayer, K., Stierschneider, M., . . . van Loo, M. (2021). Looking for the needle in a downsized haystack: Whole‐exome sequencing unravels genomic signals of climatic adaptation in Douglas‐fir (Pseudotsuga menziesii ).Ecology and Evolution .
Gilbert, K. J., & Whitlock, M. C. (2015). QST–FST comparisons with unbalanced half‐sib designs. Molecular ecology resources, 15 (2), 262-267.
Gronau, I., Hubisz, M. J., Gulko, B., Danko, C. G., & Siepel, A. (2011). Bayesian inference of ancient human demography from individual genome sequences. Nature genetics, 43 (10), 1031.
Gupta, S., Stamatoyannopoulos, J. A., Bailey, T. L., & Noble, W. S. (2007). Quantifying similarity between motifs. Genome Biology, 8 (2), 1-9.
Haerty, W., & Singh, R. S. (2006). Gene regulation divergence is a major contributor to the evolution of Dobzhansky–Muller incompatibilities between species of Drosophila. Molecular biology and evolution, 23 (9), 1707-1714.
He, Y., Xu, J., Wang, X., He, X., Wang, Y., Zhou, J., . . . Meng, X. (2019). The Arabidopsis pleiotropic drug resistance transporters PEN3 and PDR12 mediate camalexin secretion for resistance to Botrytis cinerea. The Plant Cell, 31 (9), 2206-2222.
Hodges, S. A., Whittall, J. B., Fulton, M., & Yang, J. Y. (2002). Genetics of floral traits influencing reproductive isolation between Aquilegia formosa and Aquilegia pubescens. the american naturalist, 159 (S3), S51-S60.
Irmisch, S., Zeltner, P., Handrick, V., Gershenzon, J., & Köllner, T. G. (2015). The maize cytochrome P450 CYP79A61 produces phenylacetaldoxime and indole-3-acetaldoxime in heterologous systems and might contribute to plant defense and auxin formation. BMC plant biology, 15 (1), 1-14.
Janda, T., Tajti, J., Hamow, K. Á., Marček, T., Ivanovska, B., Szalai, G., . . . Darkó, É. (2021). Acclimation of photosynthetic processes and metabolic responses to elevated temperatures in cereals.Physiologia plantarum, 171 (2), 217-231.
Johnson, S. M., Lim, F.-L., Finkler, A., Fromm, H., Slabas, A. R., & Knight, M. R. (2014). Transcriptomic analysis of Sorghum bicolor responding to combined heat and drought stress. BMC Genomics, 15 (1), 1-19.
Kim, E., & Donohue, K. (2013). Local adaptation and plasticity ofErysimum capitatum to altitude: its implications for responses to climate change. Journal of Ecology, 101 (3), 796-805.
Koussevitzky, S., Suzuki, N., Huntington, S., Armijo, L., Sha, W., Cortes, D., . . . Mittler, R. (2008). Ascorbate peroxidase 1 plays a key role in the response of Arabidopsis thaliana to stress combination. Journal of Biological Chemistry, 283 (49), 34197-34203.
Kramer, E. M. (2009). Aquilegia : a new model for plant development, ecology, and evolution. Annual review of plant biology, 60 , 261-277.
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 (6), 1547-1549.
Kuriya, S., Hattori, M., Nagano, Y., & Itino, T. (2015). Altitudinal flower size variation correlates with local pollinator size in a bumblebee‐pollinated herb, Prunella vulgaris L.(Lamiaceae).Journal of evolutionary biology, 28 (10), 1761-1769.
Langfelder, P., & Horvath, S. (2008). WGCNA: an R package for weighted correlation network analysis. BMC bioinformatics, 9 (1), 1-13.
Li, B., & Dewey, C. N. (2011). RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC bioinformatics, 12 (1), 323.
Li, H., & Durbin, R. (2009). Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics, 25 (14), 1754-1760.
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., . . . Durbin, R. (2009). The sequence alignment/map format and SAMtools.Bioinformatics, 25 (16), 2078-2079.
Li, M., Wang, H., Ding, N., Lu, T., Huang, Y., Xiao, H., . . . Li, L. (2019). Rapid divergence followed by adaptation to contrasting ecological niches of two closely related columbine speciesAquilegia japonica and A. oxysepala . Genome biology and evolution, 11 (3), 919-930.
Li, S., An, Y., Hailati, S., Zhang, J., Cao, Y., Liu, Y., . . . Yang, P. (2019). Overexpression of the cytokinin oxidase/dehydrogenase (CKX) fromMedicago sativa enhanced salt stress tolerance ofArabidopsis . Journal of Plant Biology, 62 (5), 374-386.
Liao, Q., Zhou, T., Yao, J. Y., Han, Q. F., Song, H. X., Guan, C. Y., . . . Singh, A. K. (2018). Genome-scale characterization of the vacuole nitrate transporter Chloride Channel (CLC) genes and their transcriptional responses to diverse nutrient stresses in allotetraploid rapeseed. PLoS One, 13 (12).
Lischer, H. E., & Excoffier, L. (2012). PGDSpider: an automated data conversion tool for connecting population genetics and genomics programs. Bioinformatics, 28 (2), 298-299.
Love, M., Anders, S., & Huber, W. (2014). Differential analysis of count data–the DESeq2 package. Genome Biol, 15 (550), 10.1186.
Lu, T., Li, M.-R., Ding, N., Wang, Z.-H., Lan, L.-Z., Gao, X., & Li, L.-F. (2019). Genetic and epigenetic mechanisms underpinning the adaptive radiation of Aquilegia species. bioRxiv , 782821.
Luo, Y., Erst, A. S., Yang, C.-X., Deng, J.-P., & Li, L. (2018).Aquilegia yangii (Ranunculaceae), a new species from western China. Phytotaxa, 348 (4), 289-296.
Magadlela, A., Morcillo, R. J. L., Kleinert, A., Venter, M., Steenkamp, E., & Valentine, A. (2019). Glutamate dehydrogenase is essential in the acclimation of Virgilia divaricata , a legume indigenous to the nutrient-poor Mediterranean-type ecosystems of the Cape Fynbos.Journal of plant physiology, 243 , 153053.
Mayr, E. (1947). Ecological factors in speciation. Evolution , 263-288.
McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., . . . Daly, M. (2010). The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.Genome research, 20 (9), 1297-1303.
Morente‐López, J., Lara‐Romero, C., García‐Fernández, A., Rubio Teso, M. L., Prieto‐Benítez, S., & Iriondo, J. M. (2021). Gene flow effects on populations inhabiting marginal areas: origin matters. Journal of Ecology, 109 (1), 139-153.
Mulcare, D. M. (2004). NGS Toolkit, Part 8: The National Geodetic Survey NADCON Tool. Professional Surveyor Magazine .
Munz, P. A. (1946). Aquilegia: the cultivated and the wild Columbines : Bailey Hortorium.
Nguyen, L.-T., Schmidt, H. A., Von Haeseler, A., & Minh, B. Q. (2015). IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Molecular biology and evolution, 32 (1), 268-274.
Nosil, P., & Schluter, D. (2011). The genes underlying the process of speciation. Trends in Ecology & Evolution, 26 (4), 160-167.
Omidbakhshfard, M. A., Fujikura, U., Olas, J. J., Xue, G.-P., Balazadeh, S., & Mueller-Roeber, B. (2018). GROWTH-REGULATING FACTOR 9 negatively regulates arabidopsis leaf growth by controlling ORG3 and restricting cell proliferation in leaf primordia. PLoS genetics, 14 (7), e1007484.
Pandian, B. A., Sathishraj, R., Djanaguiraman, M., Prasad, P., & Jugulam, M. (2020). Role of cytochrome P450 enzymes in plant stress response. Antioxidants, 9 (5), 454.
Patterson, N., Moorjani, P., Luo, Y., Mallick, S., Rohland, N., Zhan, Y., . . . Reich, D. (2012). Ancient admixture in human history.Genetics, 192 (3), 1065-1093.
Philippe, R. N., Ralph, S. G., Külheim, C., Jancsik, S. I., & Bohlmann, J. (2010). Poplar defense against insects: genome analysis, full-length cDNA cloning, and transcriptome and protein analysis of the poplar Kunitz-type protease inhibitor family. New Phytologist, 184 (4), 865-884.
Presgraves, D. C. (2010). The molecular evolutionary basis of species formation. Nature reviews genetics, 11 (3), 175-180.
Price, A. L., Patterson, N. J., Plenge, R. M., Weinblatt, M. E., Shadick, N. A., & Reich, D. (2006). Principal components analysis corrects for stratification in genome-wide association studies.Nature genetics, 38 (8), 904-909.
Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M. A., Bender, D., . . . Daly, M. J. (2007). PLINK: a tool set for whole-genome association and population-based linkage analyses. The American journal of human genetics, 81 (3), 559-575.
Quattrocchio, F., Wing, J., van der Woude, K., Souer, E., de Vetten, N., Mol, J., & Koes, R. (1999). Molecular analysis of the anthocyanin2 gene of petunia and its role in the evolution of flower color. The Plant Cell, 11 (8), 1433-1444.
Raman, S. (1998). Endless forms: species and speciation : Oxford University Press on Demand.
Riboni, M., Robustelli Test, A., Galbiati, M., Tonelli, C., & Conti, L. (2016). ABA-dependent control of GIGANTEA signalling enables drought escape via up-regulation of FLOWERING LOCUS T in Arabidopsis thaliana . Journal of experimental botany, 67 (22), 6309-6322.
Rieseberg, L. H., & Blackman, B. K. (2010). Speciation genes in plants.Annals of botany, 106 (3), 439-455.
Rodríguez-Celma, J., Chou, H., Kobayashi, T., Long, T. A., & Balk, J. (2019). Hemerythrin E3 Ubiquitin Ligases as Negative Regulators of Iron Homeostasis in Plants. Other, 10 .
Schwinn, K., Venail, J., Shang, Y., Mackay, S., Alm, V., Butelli, E., . . . Martin, C. (2006). A small family of MYB-regulatory genes controls floral pigmentation intensity and patterning in the genus Antirrhinum.The Plant Cell, 18 (4), 831-851.
Seong, E.-S., Choi, D.-I., Cho, H.-S., Lim, C.-K., Cho, H.-J., & Wang, M.-H. (2007). Characterization of a stress-responsive ankyrin repeat-containing zinc finger protein of Capsicum annuum (CaKR1).BMB Reports, 40 (6), 952-958.
Shu, K., Chen, F., Zhou, W., Luo, X., Dai, Y., Shuai, H., & Yang, W. (2018). ABI4 regulates the floral transition independently of ABI5 and ABI3. Molecular Biology Reports, 45 (6), 2727-2731.
Shu, K., Chen, Q., Wu, Y., Liu, R., Zhang, H., Wang, P., . . . Liu, C. (2016). ABI 4 mediates antagonistic effects of abscisic acid and gibberellins at transcript and protein levels. The Plant Journal, 85 (3), 348-361.
Shu, K., Zhang, H., Wang, S., Chen, M., Wu, Y., Tang, S., . . . Xie, Q. (2013). ABI4 regulates primary seed dormancy by regulating the biogenesis of abscisic acid and gibberellins in Arabidopsis. PLoS Genet, 9 (6), e1003577.
Smith, B. J. (2007). boa: an R package for MCMC output convergence assessment and posterior inference. Journal of statistical software, 21 (11), 1-37.
Steinthorsdottir, M., Coxall, H., De Boer, A., Huber, M., Barbolini, N., Bradshaw, C., . . . Henderiks, J. (2021). The Miocene: The future of the past. Paleoceanography and Paleoclimatology, 36 (4), e2020PA004037.
Sun, M., Schlüter, P. M., Gross, K., & Schiestl, F. P. (2015). Floral isolation is the major reproductive barrier between a pair of rewarding orchid sister species. Journal of evolutionary biology, 28 (1), 117-129.
Surya, R. (2020). In-silico characterization of At5g18130 gene inArabidopsis thaliana with emphasis on its expression patterns and functional aspects. Journal of Pharmacognosy and Phytochemistry, 9 (5), 987-995.
Tao, X., Wang, M.-X., Dai, Y., Wang, Y., Fan, Y.-F., Mao, P., & Ma, X.-R. (2017). Identification and expression profile of CYPome in perennial ryegrass and tall fescue in response to temperature stress.Frontiers in plant science, 8 , 1519.
Turbek, S. P., Browne, M., Di Giacomo, A. S., Kopuchian, C., Hochachka, W. M., Estalles, C., . . . Lovette, I. J. (2021). Rapid speciation via the evolution of pre-mating isolation in the Iberá Seedeater.science, 371 (6536).
Turelli, M., Barton, N. H., & Coyne, J. A. (2001). Theory and speciation. Trends in Ecology & Evolution, 16 (7), 330-343.
Wang, M., Yuan, J., Qin, L., Shi, W., Xia, G., & Liu, S. (2020). Ta CYP 81D5, one member in a wheat cytochrome P450 gene cluster, confers salinity tolerance via reactive oxygen species scavenging. Plant biotechnology journal, 18 (3), 791-804.
Wang, X., He, Z., Shi, S., & Wu, C.-I. (2020). Genes and speciation: is it time to abandon the biological species concept? National Science Review, 7 (8), 1387-1397.
Whittall, J. B. (2005). Ecological speciation and convergent evolution in the North American columbine radiation (Aquilegia, Ranunculaceae) : University of California, Santa Barbara.
Wu, C. I. (2001). The genic view of the process of speciation.Journal of evolutionary biology, 14 (6), 851-865.
Xu, S., Schlüter, P. M., Scopece, G., Breitkopf, H., Gross, K., Cozzolino, S., & Schiestl, F. P. (2011). Floral isolation is the main reproductive barrier among closely related sexually deceptive orchids.Evolution: International Journal of Organic Evolution, 65 (9), 2606-2620.
Yu, G., Wang, L.-G., Han, Y., & He, Q.-Y. (2012). clusterProfiler: an R package for comparing biological themes among gene clusters.Omics: a journal of integrative biology, 16 (5), 284-287.
Zhang, C., Dong, S.-S., Xu, J.-Y., He, W.-M., & Yang, T.-L. (2019). PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format files. Bioinformatics, 35 (10), 1786-1788.
Zhang, W., Wang, H., Dong, J., Zhang, T., & Xiao, H. (2021). Comparative chloroplast genomes and phylogenetic analysis of Aquilegia.Applications in plant sciences, 9 (3), e11412.
Zhao, Z., Heideman, N., Bester, P., Jordaan, A., & Hofmeyr, M. D. (2020). Climatic and topographic changes since the Miocene influenced the diversification and biogeography of the tent tortoise (Psammobates tentorius) species complex in Southern Africa. BMC evolutionary biology, 20 (1), 1-33.
Zheng, Y., Huang, Y., Xian, W., Wang, J., & Liao, H. (2012). Identification and expression analysis of the Glycine max CYP707A gene family in response to drought and salt stresses. Annals of botany, 110 (3), 743-756.