Distinct teosinte hybrid zones and genomic architectures of hybridization
Hybridization is a major force of evolution and has profound consequences due to increased heterozygosity and the creation of novel allele combinations. Hybrid zones form when allopatric taxa meet in secondary contact and hybridize. These allele combinations can be random, but sometimes alleles are retained nonrandomly leading to genomic architectures of hybridization. Genomic architectures of hybridization can be the product of natural selection, especially when present at significantly higher levels than expected by chance. Here we used three SNP data sets to identify hybrids in four genotypically distinct putative hybrid zones with unique environments. We identified genomic architectures of hybridization at the population, hybrid group, and all hybrids levels. We also found evidence for adaptation of hybrids to elevation and identified two hybrid populations that would be ideal for seeking direct evidence of local adaptation. We also developed SequelTools, which is a collection of tools for working with PacBio Sequel raw sequence data. This research in teosinte hybrids provides the hybridization and hybrid zone communities an excellent model study system and the creation of SequelTools makes using PacBio data much easier, which will help a large and diverse set of researchers take advantage of this powerful sequencing technology. 1 CHAPTER 1. GENERAL INTRODUCTION Hybridization is a powerful evolutionary force that creates high levels of heterozygosity and new allele combinations resulting in improved adaptive potential (Barton and Hewitt, 1985; Abbott et al. 2008) Hybridization can also result in the creation of invasive species (Abbott et al. 2008) lead to hybrid speciation, or even threaten parental taxa with extinction when forming hybrid swarms (Allendorf et al. 2001; Rhymer and Simberloff, 1996) Hybrid zones are regions were diverged parental taxa come into secondary contact and form hybrids (Barton and Hewitt, 1985) Hybrid zones have been extensively studied in a wide variety of species (Gimnez et al. 2016; Rieseberg et al. 1999; Brennan et al. 2009; Mallet et al. 1990; Taylor et al. 2014; Mandeville et al. 2017; Parchman et al. 2013) Replicate hybrids zones between the same parental taxa have received less attention, but are an excellent opportunity for the study of natural selection as it acts upon diverse pools of alleles across a range of environments. Recombination constantly breaks up and scrambles these allele combinations in hybrid populations, but sometimes certain alleles are retained at heightened frequencies in a given hybrid population due to their local selective advantage, resulting in distinct genomic architectures of hybridization (GAHs) (Barton and Hewitt, 1985; Smith and O'brien, 2005; Abbott et al. 2013; Buerkle and Rieseberg, 2001; Nolte et al. 2009) Zea mays ssp. parviglumis (hereafter parviglumis) and Zea mays ssp. mexicana (hereafter mexicana) are particularly well suited for studying hybridization and GAHs. Parviglumis is the progenitor of maize (Matsuoka et al. 2002) a major international crop, which means that understanding this wild grass may provide agronomic benefits. Mexicana has an important relationship to maize as it assisted maize's spread through the Americas via introgression (da Fonseca et al. 2015; Hufford et al. 2013) Parviglumis is native to the 2 lowlands of Central Mexico and Mexicana is native to nearby highland habitats (Wilkes, 1967; Hufford et al. 2012b) Furthermore, there is evidence that parviglumis and mexicana have adapted to their respective environments in terms of factors associated with altitude (Wilkes, 1967; Doebley, 1984) Parviglumis and mexicana are diverse, perhaps more generally representative of flowering plants than model species such as Arabidopsis, and have been shown to be locally adapted (Hufford et al. 2012a; Ross Ibarra et al. 2009) Hybrids have also been discovered previously between Parviglumis and Mexicana (Fukunaga et al. 2005; Hufford et al. 2012b; Van Heerwaarden et al. 2011; Pyhajarvi et al. 2013) An additional important component of my training in Bioinformatics, and a requirement of the Bioinformatics and Computational Biology PhD program, is that I develop a software tool. 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