Harrison RG. Hybrid zones: window on evolutionary process. Oxf Surv Evol Biol. 1990; 7:69–128.
Google Scholar
Harrison RG. Hybrid Zones and the Evolutionary Process.New York: Oxford University Press; 1993, p. 364.
Google Scholar
Rieseberg LH, Kim S-C, Randell Ra, Whitney KD, Gross BL, Lexer C, Clay K. Hybridization and the colonization of novel habitats by annual sunflowers. Genetica. 2007; 129(2):149–65. https://doi.org/10.1007/s10709-006-9011-y.
Rieseberg LH, Willis JH. Plant Speciation. Science. 2007; 317(5840):910–4. https://doi.org/10.1126/science.1137729.
Rieseberg LH. Evolution: Replacing genes and traits through hybridization. Curr Biol. 2009; 19(3):119–22. https://doi.org/10.1016/j.cub.2008.12.016.
Kenney AM, Sweigart AL, Kenney AM. Reproductive isolation and introgression between sympatric Mimulus species. Mol Ecol. 2016. https://doi.org/10.1111/mec.13630.
Levin DA, Francisco-Ortega J, Jansen RK. Hybridization and the extinction of rare plant species. Conserv Biol. 1995; 10(1):10–6.
Article
Google Scholar
Allendorf FW, Leary RF, Spruell P, Wenburg JK. The problems with hybrids: Setting conservation guidelines. Trends Ecol Evol. 2001; 16(11):613–22. https://doi.org/10.1016/S0169-5347(01)02290-X.
Lotsy JP. Evolution by Means of Hybridization.Zeitschrift für Induktive Abstammungs-und Vererbungslehre. 1918; 20.1:42–5.
Google Scholar
Anderson E.Introgressive hybridization. Biol Rev. 1953; 28(3):280–307.
Article
Google Scholar
Barton NH, Hewitt GM. Analysis of hybrid zones. Annu Rev Ecol Syst. 1985; 16(1):113–48. https://doi.org/10.1146/annurev.es.16.110185.000553.
Mecham JS. Introgressive hybridization between two southeastern treefrogs. Evolution. 1960; 14(4):445–57.
Article
Google Scholar
Yang S, Selander RK. Hybridization in the grackle Quiscalus quiscula in Louisiana. Syst Zool. 1968; 17(2):107–43.
Article
CAS
PubMed
Google Scholar
Turner JRG. Two thousand generations of hybridisation in a Heliconius butterfly. Evolution. 1971; 25(3):471–82.
Article
PubMed
Google Scholar
Atchley WR, Hensleigh DA. The congruence of morphometric shape in relation to genetic divergence in four races of morabine grasshoppers (Orthoptera: Eumastacidae). Evolution. 1974; 28(3):416–27.
Article
PubMed
Google Scholar
Heiser CB. Study in the Evolution of the sunflower species Helianthus Annuus and H. Bolanderi.Univ Calif Publ Bot. 1949; 23:157–208.
Google Scholar
Rollins RC. Interspecific hybridization and taxon uniformity in Arabis (Cruciferae). Am J Bot. 1983; 70(4):625–34.
Article
Google Scholar
Moran C, Wilkinson P, Shaw D. Allozyme variation across a narrow hybrid zone in the grasshopper, Caledia captiva. Heredity. 1980; 44(1):69–81.
Article
Google Scholar
Hunter RL, Markert CL. Histochemical demonstration of enzymes separated by zone electrophoresis in starch gels. Science. 1957; 125(3261):1294–5.
Article
CAS
PubMed
Google Scholar
Feder JH. Natural hybridization and genetic divergence between the toads Bufo boreas and Bufo punctatus. Evolution. 1979; 33(4):1089–97.
Article
PubMed
Google Scholar
Baker RJ, Bickham JW, Arnold ML. Chromosomal evolution in Rhogessa (Chiroptera: Vespertilionidae): Possible speciation by centric fusions. Evolution. 1985; 39(2):233–43.
Article
PubMed
Google Scholar
Edwards A, Civitello A, Hammond HA, Caskey CT. DNA typing and genetic mapping with trimeric and tetrameric tandem repeats. Am J Hum Genet. 1991; 49(4):746–56.
CAS
PubMed
PubMed Central
Google Scholar
Botstein D, White RL, Skolnick M, Davis RW. Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet. 1980; 32(3):314–31.
CAS
PubMed
PubMed Central
Google Scholar
Williams JG, Kubelik AR, Livak KJ, Rafalski JA, Tingey SV. DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res. 1990; 18(22):6531–5. https://doi.org/10.1093/nar/18.22.6531.
Vos P, Hogers R, Bleeker M, Reijans M, van de Lee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M. A new technique for DNA fingerprinting. Nucleic Acids Res. 1995; 44(21):388–96.
Google Scholar
Arnold ML, Emms SK. Molecular markers, gene flow, and natural selection. In: Molecular Systematics of Plants II: DNA Sequencing. New York: Springer: 1998. p. 442–58.
Google Scholar
Rieseberg LH. Genetic Mapping as a Tool for Studying Speciation. In: Molecular Systematics of Plants II: DNA Sequencing. New York: Springer: 1998. p. 459–87. Chap. 16.
Google Scholar
Elshire RJ, Glaubitz JC, Sun Q, Poland Ja, Kawamoto K, Buckler ES, Mitchell SE. A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS ONE. 2011; 6(5):19379. https://doi.org/10.1371/journal.pone.0019379.
Parchman TL, Gompert Z, Mudge J, Schilkey FD, Benkman CW, Buerkle CA. Genome-wide association genetics of an adaptive trait in lodgepole pine. Mol Ecol. 2012; 21(12):2991–3005. https://doi.org/10.1111/j.1365-294X.2012.05513.x.
Gompert Z, Lucas LK, Buerkle CA, Forister ML, Fordyce JA, Nice CC. Admixture and the organization of genetic diversity in a butterfly species complex revealed through common and rare genetic variants. Mol Ecol. 2014; 23(18):4555–73. https://doi.org/10.1111/mec.12811.
Brumfield RT, Beerli P, Nickerson Da, Edwards SV. The utility of single nucleotide polymorphisms in inferences of population history. Trends Ecol Evol. 2003; 18(1):249–56. https://doi.org/10.1016/S0169-5347(03)00018-1.
Liu N, Chen L, Wang S, Oh C, Zhao H. Comparison of single-nucleotide polymorphisms and microsatellites in inference of population structure. BMC Genet. 2005; 6(1):26. https://doi.org/10.1186/1471-2156-6-S1-S26.
Xing C, Schumacher FR, Xing G, Lu Q, Wang T, Elston RC. Comparison of microsatellites, single-nucleotide polymorphisms (SNPs) and composite markers derived from SNPs in linkage analysis. BMC Genet. 2005; 6 Suppl 1(Ic):29. https://doi.org/10.1186/1471-2156-6-S1-S29.
Ball AD, Stapley J, Dawson Da, Birkhead TR, Burke T, Slate J. A comparison of SNPs and microsatellites as linkage mapping markers: lessons from the zebra finch (Taeniopygia guttata). BMC Genomics. 2010; 11:218. https://doi.org/10.1186/1471-2164-11-218.
Buerkle CA, Gompert Z. Population genomics based on low coverage sequencing: how low should we go?Mol Ecol. 2013; 22:3028–35. https://doi.org/10.1111/mec.12105.
Gompert Z, Buerkle CA. Analyses of genetic ancestry enable key insights for molecular ecology. Mol Ecol. 2013; 22(21):5278–94. https://doi.org/10.1111/mec.12488.
Jeffries DL, Copp GH, Lawson Handley L-J, Olsén H, Sayer CD, Hänfling B. Comparing RADseq and microsatellites to infer complex phylogeographic patterns, a real data informed perspective in the Crucian carp, Carassius carassius, L bioRxiv. 2015;:025973. https://doi.org/10.1101/025973.
Li H. A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics. 2011; 27(21):2987–93. https://doi.org/10.1093/bioinformatics/btr509.
Skotte L, Korneliussen TS, Albrechtsen A. Estimating individual admixture proportions from Next-generation sequencing data. Genetics. 2013; 195:1–28. https://doi.org/10.1534/genetics.113.154138.
Böcher TW. Cytological and embryological studies in the amphi-apomictic Arabis holboellii complex. Kongel.Danske Vidensk.-Selskab.Biol.Skr. 1951; 6:1–59.
Google Scholar
Rollins RC. Studies on Arabis (Cruciferae) of western North America. Syst Bot. 1981; 6(May 1948):55–64.
Article
Google Scholar
Roy BA. The breeding systems of six species of Arabis (Brassicaceae). Am J Bot. 1995; 82(7):869–77.
Article
Google Scholar
Li F-W, Rushworth CA, Beck JB, Windham MD. Boechera Microsatellite Website: an online portal for species identification and determining hybrid parentage. Database: baw169. 2017. http://sites.biology.duke.edu/windhamlab/main.html.
Alexander PJ, Windham MD, Beck JB, Al-Shehbaz IA, Bailey CD. Molecular phylogenetics and taxonomy of the genus Boechera and related genera (Brassicaceae: Boechereae). Syst Bot. 2013; 38(1):192–209.
Article
Google Scholar
Koch M, Al-Shehbaz IA, Mummenhoff K. Molecular systematics, evolution, and population biology in the mustard family (Brassicaceae). Ann Missouri Bot Gard. 2003; 90:151–71.
Article
Google Scholar
Dobeš CH, Mitchell-Olds T, Koch MA. Extensive chloroplast haplotype variation indicates Pleistocene hybridization and radiation of North American Arabis drummondii, A. x divaricarpa, and A. holboellii (Brassicaceae). Mol Ecol. 2004; 13:349–70. https://doi.org/10.1046/j.1365-294X.2003.02064.x.
Dobeš C, Mitchell-Olds T, Koch MA. Intraspecific diversification in North American Boechera stricta (= Arabis drummondii), Boechera x divaricarpa, and Boechera holboellii (Brassicaceae) inferred from nuclear and chloroplast molecular markers - An integrative approach. Am J Bot. 2004; 91(12):2087–101.
Article
PubMed
Google Scholar
Song B-H, Clauss MJ, Pepper A, Mitchell-Olds T. Geographic patterns of microsatellite variation in Boechera stricta, a close relative of Arabidopsis. Mol Ecol. 2006; 15(2):357–69. https://doi.org/10.1111/j.1365-294X.2005.02817.x.
Song B-H, Mitchell-Olds T. High genetic diversity and population differentiation in Boechera fecunda, a rare relative of Arabidopsis. Mol Ecol. 2007; 16(19):4079–88. https://doi.org/10.1111/j.1365-294X.2007.03500.x.
Naumova TN, Van der Laak J, Osadtchiy J, Matzk F, Kravtchenko A, Bergervoet J, Ramulu KS, Boutilier K. Reproductive development in apomictic populations of Arabis holboellii (Brassicaceae). Sex Plant Reprod. 2001; 14(4):195–200. https://doi.org/10.1007/s00497-001-0118-0.
Aliyu OM, Schranz ME, Sharbel TF. Quantitative variation for apomictic reproduction in the genus Boechera (Brassicaceae). Am J Bot. 2010; 97(10):1719–31. https://doi.org/10.3732/ajb.1000188.
Nogler GA. Gametophytic apomixis In: Johri BM, editor. Embryology of Angiosperms. Berlin & Heidelberg: Springer: 1984. p. 475–518. Chap. 10.
Google Scholar
Schranz ME, Dobeš C, Koch MA, Mitchell-Olds T. Sexual reproduction, hybridization, apomixis, and polyploidization in the genus Boechera (Brassicaceae). Am J Bot. 2005; 92(11):1797–810.
Article
CAS
PubMed
Google Scholar
Dobeš C, Sharbel TF, Koch M. Towards understanding the dynamics of hybridization and apomixis in the evolution of the genus Boechera (Brassicaceae). Syst Biodivers. 2007; 5(3):321–31. https://doi.org/10.1017/S1477200007002423.
Beck JB, Alexander PJ, Allphin L, Al-Shehbaz IA, Rushworth C, Bailey CD, Windham MD. Does hybridization drive the transition to asexuality in diploid Boechera?Evolution. 2011; 66(4):985–95. https://doi.org/10.1111/j.1558-5646.2011.01507.x.
Windham MD, Beck JB, Li F-W, Allphin L, Carman JG, Sherwood DA, Rushworth CA, Sigel E, Alexander PJ, Bailey CD, et al. Searching for diamonds in the apomictic rough: a case study involving Boechera lignifera (Brassicaceae). Syst Botany. 2016; 40(4):1031–44.
Article
Google Scholar
Windsor AJ, Schranz ME, Formanova N, Gebauer-Jung S, Bishop JG, Schnabelrauch D, Kroymann J, Mitchell-Olds T. Partial shotgun sequencing of the Boechera stricta genome reveals extensive microsynteny and promoter conservation with Arabidopsis. Plant Physiol. 2006; 140(April):1169–82. https://doi.org/10.1104/pp.105.073981.2.
Schranz ME, Song B-H, Windsor AJ, Mitchell-Olds T. Comparative genomics in the Brassicaceae: a family-wide perspective. Curr Opin Plant Biol. 2007; 10(2):168–75. https://doi.org/10.1016/j.pbi.2007.01.014.
Kantama L, Sharbel TF, Schranz ME, Mitchell-Olds T, de Vries S, de Jong H. Diploid apomicts of the Boechera holboellii complex display large-scale chromosome substitutions and aberrant chromosomes. Proc Natl Acad Sci USA. 2007; 104(35):14026–31. https://doi.org/10.1073/pnas.0706647104.
Mandáková T, Schranz ME, Sharbel TF, de Jong H, Lysak MA. Karyotype evolution in apomictic Boechera and the origin of the aberrant chromosomes. Plant J. 2015; 82:785–93. https://doi.org/10.1111/tpj.12849.
Knight CA, Vogel H, Kroymann J, Shumate A, Witsenboer H, Mitchell-Olds T. Expression profiling and local adaptation of Boechera holboellii populations for water use efficiency across a naturally occurring water stress gradient. Mol Ecol. 2006; 15(5):1229–37. https://doi.org/10.1111/j.1365-294X.2006.02818.x.
Anderson JT, Lee C-R, Mitchell-olds T. Life history and natural selection on flowering time in Boechera stricta, a perennial relative of Arabidopsis. Evolution. 2011; 65(3):771–87. https://doi.org/10.1111/j.1558-5646.2010.01175.x.Life.
Lee C-R, Mitchell-Olds T. Complex trait divergence contributes to environmental niche differentiation in ecological speciation of Boechera stricta. Mol Ecol. 2013. https://doi.org/10.1111/mec.12250.
Anderson JT, Lee C-R, Rushworth CA, Colautti RI, Mitchell-Olds T. Genetic trade-offs and conditional neutrality contribute to local adaptation. Mol Ecol. 2013; 22(3):699–708. https://doi.org/10.1111/j.1365-294X.2012.05522.x.
Anderson JT, Lee C-R, Mitchell-Olds T. Strong selection genome-wide enhances fitness trade-offs across environments and episodes of selection. Evolution. 2014; 68(1):16–31. https://doi.org/10.1111/evo.12259.
Anderson JT, Perera N, Chowdhury B, Mitchell-Olds T. Microgeographic patterns of genetic divergence and adaptation across environmental gradients in Boechera stricta (Brassicaceae). Am Nat. 2015; 186:(October). https://doi.org/10.1086/682404.
Carman J. Asynchronous expression of duplicate genes in angiosperms may cause apomixis, bispory, tetraspory, and polyembryony. Biol J Linn Soc. 1997; 61(1):51–94. https://doi.org/10.1006/bijl.1996.0118.
Schmidt A, Schmid MW, Grossniklaus U. Plant germline formation: common concepts and developmental flexibility in sexual and asexual reproduction. Development. 2015; 142:229–41. https://doi.org/10.1242/dev.102103.
Sharbel TF, Voigt M-L, Corral JM, Galla G, Kumlehn J, Klukas C, Schreiber F, Vogel H, Rotter B. Apomictic and sexual ovules of Boechera display heterochronic global gene expression patterns. Plant Cell. 2010; 22(3):655–71. https://doi.org/10.1105/tpc.109.072223.
Song B-H, Windsor AJ, Schmid KJ, Ramos-Onsins S, Schranz ME, Heidel AJ, Mitchell-Olds T. Multilocus patterns of nucleotide diversity, population structure and linkage disequilibrium in Boechera stricta, a wild relative of Arabidopsis. Genetics. 2009; 181(3):1021–33. https://doi.org/10.1534/genetics.108.095364.
Rushworth CA, Song B-H, Lee C-R, Mitchell-Olds T. Boechera, a model system for ecological genomics. Mol Ecol. 2011; 20(23):4843–57. https://doi.org/10.1111/j.1365-294X.2011.05340.x.
Alexander PJ, Windham MD, Beck JB, Al-Shehbaz IA, Bailey CD. Weaving a tangled web: Divergent and reticulate speciation in Boechera fendleri sensu lato (Brassicaceae: Boechereae). Syst Bot. 2015; 40(2):572–96. https://doi.org/10.1600/036364415X688745.
MPS scripts for high-throughput sequencing repository. http://github.com/schimar/hts_tools. Accessed 12 Aug 2015.
B. stricta genome assembly. DOE-JGI Phytozome. http://phytozome.jgi.doe.gov. Accessed 24 June 2015.
Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009; 25(14):1754–60. https://doi.org/10.1093/bioinformatics/btp324.
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009; 25(16):2078–9. https://doi.org/10.1093/bioinformatics/btp352.
McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo Ma. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010; 20(9):1297–303. https://doi.org/10.1101/gr.107524.110.
Franzke A, Koch MA, Mummenhoff K. Turnip time travels: Age estimates in Brassicaceae. Trends Plant Sci. 2016. https://doi.org/10.1016/j.tplants.2016.01.024.
Paradis E, Claude J, Strimmer K. APE: Analyses of Phylogenetics and Evolution in R language. Bioinformatics. 2004; 20(2):289–90.
Article
CAS
PubMed
Google Scholar
Falush D, Stephens M, Pritchard JK. Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics. 2003; 164(4):1567–87.
CAS
PubMed
PubMed Central
Google Scholar
Jombart T, Devillard S, Balloux F. Discriminant analysis of principal components: a new method for the analysis of genetically structured populations. BMC Genet. 2010; 11:94. https://doi.org/10.1186/1471-2156-11-94.
Jombart T. adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics. 2008; 24(11):1403–5. https://doi.org/10.1093/bioinformatics/btn129.
Jombart T, Ahmed I. adegenet 1.3-1: new tools for the analysis of genome-wide SNP data. Bioinformatics. 2011; 27(21):3070–1. https://doi.org/10.1093/bioinformatics/btr521.
Alexander DH, Novembre J, Lange K. Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 2009;:1655–64. https://doi.org/10.1101/gr.094052.109.vidual.
Falush D, van Dorp L, Lawson DJ. A tutorial on how (not) to over-interpret STRUCTURE / ADMIXTURE bar plots. bioRxiv. 2016. https://doi.org/10.1101/066431.
Gelman A, Rubin DB. lnference from iterative simulation using multiple sequences. Stat Sci. 1992; 7(4):457–72. https://doi.org/10.2307/2246093.
Plummer M, Best N, Cowles K, Vines K. CODA: convergence diagnosis and output analysis for MCMC. R News. 2006; 6(March):7–11. https://doi.org/10.1159/000323281.
R Development Core Team: An Introduction to R. Vienna: R Foundation for Statistical Computing; 2015. http://www.r-project.org.
Pickrell JK, Pritchard JK. Inference of population splits and mixtures from genome-wide allele frequency data. PLoS Genet. 2012; 8(11):1002967. https://doi.org/10.1371/journal.pgen.1002967.
Kiefer C, Koch MA. A continental-wide perspective: the genepool of nuclear encoded ribosomal DNA and single-copy gene sequences in North American Boechera (Brassicaceae). PLoS ONE. 2012; 7(5):36491. https://doi.org/10.1371/journal.pone.0036491.
Al-Shehbaz IA, Windham MD. Boechera In: Flora of North America Committee, editor. Flora of North America, North of Mexico. 7th ed. New York and Oxford: Oxford University Press: 2010. p. 347–412.
Lovell JT, Aliyu OM, Mau M, Schranz ME, Koch M, Kiefer C, Song B-H, Mitchell-Olds T, Sharbel TF. On the origin and evolution of apomixis in Boechera. Plant Reprod. 2013; 26(4):309–15. https://doi.org/10.1007/s00497-013-0218-7.
Asker S, Jerling L. Apomixis in Plants. Boca Raton and London: CRC Press; 1992.
Google Scholar
Sharbel TF, Mitchell-Olds T. Recurrent polyploid origins and chloroplast phylogeography in the Arabis holboellii complex (Brassicaceae). Heredity. 2001; 87(1):59–68. https://doi.org/10.1046/j.1365-2540.2001.00908.x.
Mau M, Lovell JT, Corral JM, Kiefer C, Koch Ma, Aliyu OM, Sharbel TF. Hybrid apomicts trapped in the ecological niches of their sexual ancestors. Proc Natl Acad Sci USA. 2015; 112:201423447. https://doi.org/10.1073/pnas.1423447112.
Wood TE, Takebayashi N, Barker MS, Mayrose I, Greenspoon PB, Rieseberg LH. The frequency of polyploid speciation in vascular plants. Proc Natl Acad Sci USA. 2009; 106(33):13875–9. https://doi.org/10.1073/pnas.0811575106.
Barrett SCH. Evolution of mating systems: Outcrossing versus selfing. In: The Princeton Guide to Evolution. Oxford: Princeton University Press: 2014. p. 356–62.
Google Scholar
Lien S, Koop BF, Sandve SR, Miller JR, Matthew P, Leong JS, Minkley DR, Zimin A, Grammes F, Grove H, Gjuvsland A, Walenz B, Hermansen RA, Schalburg KV, Rondeau EB, Genova AD, Samy JKA, Vik JO. The Atlantic salmon genome provides insights into rediploidization. Nature. 2016;6020. https://doi.org/10.1038/nature17164.
Mandakova T, Gloss AD, Whiteman NK, Lysak MA. How diploidization turned a tetraploid into a pseudotriploid. Am J Bot. 2016; 103(2014):1–10. https://doi.org/10.3732/ajb.1500452.