Historical Divergence and Gene Flow in the Genus Zea

Abstract

Gene flow plays a fundamental role in plant evolutionary history, yet its role in population divergence-and ultimately speciation-remains poorly understood. We investigated gene flow and the modalities of divergence in the domesticate Zea mays ssp. mays and three wild Zea taxa using sequence polymorphism data from 26 nuclear loci. We described diversity across loci and assessed evidence for adaptive and purifying selection at nonsynonymous sites. For each of three divergence events in the history of these taxa, we used approximate Bayesian simulation to estimate population sizes and divergence times and explicitly compare among alternative models of divergence. Our estimates of divergence times are surprisingly consistent with previous data from other markers and suggest rapid diversification of lineages within Zea in the last $150,000 years. We found widespread evidence of historical gene flow, including evidence for divergence in the face of gene flow. We speculate that cultivated maize may serve as a bridge for gene flow among otherwise allopatric wild taxa.

Megabase-Scale Inversion Polymorphism in the Wild Ancestor of Maize

“…Fifth, the lack of rare variants and the high frequency of the most common Inv1n-I haplotype (Figure 2) suggest that this haplotype may have recently risen to high frequency due to a partial sweep. The observed lack of rare variants is especially striking given the genome-wide pattern of an excess of low-frequency variants (Table 1), an observation reported in multiple studies (Tenaillon et al 2004;Wright et al 2005;Moeller et al 2007;Ross-Ibarra et al 2009). While the most common haplotype at Inv1n-I does not show signs of extended homozygosity beyond the borders of the inversion ( Figure S5) as might be expected if it has been recently swept to higher frequency, the nearest flanking SNPs are 1.1 and 14.6 Mb distant and our power to detect an extended haplotype is low.…”

Independent Molecular Basis of Convergent Highland Adaptation in Maize

“…Selection from standing variation should be common when the scaled mutation rate u (product of the effective population size, mutation rate, and target size) is .1, as long as the scaled selection coefficient Ns (product of the effective population size and selection coefficient) is reasonably large (Hermisson and Pennings 2005). Estimates of u from synonymous nucleotide diversity in maize (Tenaillon et al 2004;Wright et al 2005;Ross-Ibarra et al 2009) suggest that adaptation from standing genetic variation may be likely for target sizes larger than a few hundred nucleotides. In maize, such a scenario has been recently shown for the locus grassy tillers1 (Wills et al 2013), at which adaptive variants in both an upstream control region and the 39-UTR are segregating in teosinte but show evidence of recent selection in maize, presumably due to the effects of this locus on branching and ear number.…”

“…N A was set to 150,000, using estimates of the composite parameter 4N A m $ 0:018 from parviglumis (Eyre-Walker et al 1998;Tenaillon et al 2001Tenaillon et al , 2004Wright et al 2005;Ross-Ibarra et al 2009) (Perry et al 2006;Grobman et al 2012); and t mex ¼ 60; 000; N mex ¼ 160; 000 (Ross-Ibarra et al 2009), and P mex ¼ 0:2 (van Heerwaarden et al 2011) for model IB. For both models IA and IB, we inferred three parameters (a, b, and g), and, for model II, we fixed t F ¼ 6000 and t G ¼ 4000 (Perry et al 2006;Piperno 2006;Grobman et al 2012) and estimated the remaining four parameters (a, b 1 ; b 2 ; and g).…”

“…Z. mays ssp. mexicana (hereafter mexicana) is native to the highlands of central Mexico, where it is thought to have occurred since at least the last glacial maximum (Ross-Ibarra et al 2009;Hufford et al 2012a). Phenotypic differences between mexicana and the lowland parviglumis mirror those between highland and lowland maize (Lauter et al 2004), and population genetic analyses of the two subspecies reveal evidence of natural selection associated with altitudinal differences (Fang et al 2012;Pyhäjärvi et al 2013).…”

Inbreeding drives maize centromere evolution

“…Several quantitative trait loci (QTLs) responsible for these morphological changes were identified in pioneering work (5)(6)(7)(8), and a large number of additional genetic loci involved in maize domestication and improvement were subsequently identified in genome-wide scans (9). Gene (and centromere) flow between the fully interfertile maize and teosinte subspecies has been documented (10,11). Functional centromeres of maize consist of 1-2 Mb of DNA enriched for the tandemly arranged CentC repeat and members of the centromeric retrotransposon (CR) family (12), which are widely distributed in seed plants and have been extensively characterized (13)(14)(15)(16)(17)(18).…”